Benchmark

.gitignore

@@ -6,4 +6,5 @@ docs
 renv.lock
 .renvignore
 .Rprofile
-renv
+renv
+inst/doc

CONTRIBUTING.md

@@ -0,0 +1,88 @@
+
+# Contributing to `corrp`
+
+Thank you for your interest in contributing to the `corrp` package!
+
+. We welcome contributions and improvements from the community. To help make the process smooth, please follow the guidelines outlined below.
+
+## How to Contribute
+
+### Reporting Bugs
+
+If you encounter a bug or issue, please follow these steps:
+1. **Search for existing issues** to see if the bug has already been reported.
+2. If not, **open a new issue** on the [GitHub Issues page](https://github.com/meantrix/corrp/issues).
+3. Be sure to include the following details:
+   - A description of the issue.
+   - Steps to reproduce the issue.
+   - Any error messages or warnings.
+   - The version of the package you're using.
+   - The R version.
+   - Operating system if relevant.
+
+
+### Submitting Code
+
+To submit code changes, please follow these steps:
+1. **Fork the repository**.
+2. **Create a new branch** for your changes.
+3. **Implement your changes**. Be sure to:
+   - Write clear and concise commit messages.
+   - Document new code and functions using `roxygen2` comments.
+   - Ensure your code follows the existing code style (e.g., indentation, naming conventions).
+
+4. **Run tests** to ensure your changes work as expected. To do this, use the following command:
+
+```R
+rcmdcheck::rcmdcheck()
+```
+
+The result should show **one note** only, like this:
+
+```
+── R CMD check results ────────────────────────────────────────────────────────────────────────────────────────────────────────────────── corrp 0.5.0 ────
+Duration: 57.5s
+
+❯ checking installed package size ... NOTE
+    installed size is 5.9Mb
+    sub-directories of 1Mb or more:
+      libs 5.6Mb
+
+0 errors ✔ | 0 warnings ✔ | 1 note ✖
+```
+
+Make sure there are **no errors** or **warnings** in the output. If there are, please resolve them before submitting your changes.
+
+1. **Push your changes** to your fork and create a pull request to the main repository.
+
+### Code Style Guidelines
+
+- **Indentation**: Use 2 spaces for indentation.
+- **Naming conventions**: Follow the existing naming conventions in the codebase.
+- **Documentation**: Document all public functions with `roxygen2` comments.
+- **Testing**: Ensure that your changes are covered by tests, especially if you're adding new functionality or fixing bugs.
+
+
+
+### Running Tests
+
+We use [testthat](https://cran.r-project.org/web/packages/testthat/index.html) for unit testing. To run the tests, use the following command:
+
+```R
+devtools::test()
+```
+
+Make sure all tests pass before submitting your changes.
+
+### Documentation
+
+If your changes introduce new functionality, make sure to:
+- Update the relevant documentation using `roxygen2` comments.
+- Update the `README.md` and any relevant vignettes.
+- Update the `NEWS.md` with your changes.
+- Update the version of the package.
+
+### License
+
+By contributing, you agree that your contributions will be licensed according to [license](LICENSE.md).
+

DESCRIPTION

@@ -17,25 +17,29 @@ Description: Compute multiple types of correlation analyses, including
     the average correlation clustering algorithm and distance 
     correlation t-test.
 Imports: 
-    Rcpp (>= 1.0.4.6),
-    RcppArmadillo (>= 0.11.2.0.0),
-    lsr (>= 0.5),
-    parallel (>= 3.6.3),
-    stats (>= 3.6.3),
-    caret (>= 6.0-85),
-    minerva (>= 1.5.8),    
-    checkmate (>= 2.0.0),
+    Rcpp (>= 1.0.13-1),
+    RcppArmadillo (>= 14.2.2-1),
+    corrplot (>= 0.95),
+    lsr (>= 0.5.2),
+    parallel (>= 4.4.1),
+    stats (>= 4.4.1),
+    caret (>= 7.0-1),
+    minerva (>= 1.5.10),
+    checkmate (>= 2.3.2),
     ppsr (>= 0.0.2),
     DescTools (>= 0.99.40)
 Suggests: 
-    corrplot,
     energy,
+    knitr,
+    rmarkdown,
     testthat
 License: GPL (>= 3)
 Encoding: UTF-8
 LazyData: true
 LinkingTo: Rcpp, RcppArmadillo
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
+Roxygen: list(markdown = TRUE)
 URL: https://github.com/meantrix/corrp,
     https://meantrix.github.io/corrp/
 BugReports: https://github.com/meantrix/corrp/issues
+VignetteBuilder: knitr

NAMESPACE

@@ -13,14 +13,17 @@ S3method(corr_rm,matrix)
 S3method(sil_acca,acca_list)
 S3method(sil_acca,list)
 export(acca)
+export(assert_required_argument)
 export(best_acca)
 export(corr_fun)
 export(corr_matrix)
 export(corr_rm)
 export(corrp)
 export(dcorT_test)
 export(ptest)
+export(set_arguments)
 export(sil_acca)
 importFrom(Rcpp,evalCpp)
 importFrom(RcppArmadillo,armadillo_version)
+importFrom(corrplot,corrplot)
 useDynLib(corrp, .registration=TRUE)

NEWS.md

@@ -1,5 +1,31 @@
 # CHANGELOG
 
+
+## 0.6.0
+
+- Add `VignetteBuilder: knitr` to DESCRIPTION
+- Add usefull error message for required parameters.
+- Fix C++ `Astar` method.
+- Run benchmarks, expand the paper to include statements on resource-intensive options, and incorporate an enhanced version of `energy::dcorT.test`. Also, change the data used in the paper.
+
+
+### Methods Added
+
+-  Added method `set_arguments`: Assigns provided arguments from the `args_list` to the parent environment. If an argument is inside the arguments of the methods that calculate statistics, it assigns it on the parent environment, and removes the argument from the list.
+-  Added method `assert_required_argument`: Ensures that a required argument is provided. If the argument is missing, it throws an error with a clear message.
+
+### Methods Altered
+
+- Altered messages and make *.args lists be able to alter arguments (`p.value`, `comp`, "alternative", "num.s", "rk") of methods: `.corlm`, `.cramersvp`, `.dcorp`, `.corperp`, `.micorp`, `.uncorp`, `.corpps`.
+- Update the `.corpps` method to support p-value testing (`p-test`), which is disabled by default due to its slow performance. When `p-test` is not performed, the `isig` value is set to `NA`. `p-test` can be run assigning an element `ptest = TRUE` to `pps.args` argument.
+
+### Documentation
+
+- Enhanced the documentation for `corrp` by including examples, refining the pair type section with additional details and references, and providing a more comprehensive explanation of the output format and its interpretation.
+- Improved the documentation for `corr_rm` by adding examples and providing a clearer explanation of the `c` parameter.
+- Added examples of usage in the documentation for: `acca`, `best_acca`, `corrp`, `corr_rm`, `corr_matrix`, `corr_fun`, `ptest`, `sil_acca`.
+
+
 ## 0.5.0
 
 - Creates the package website with the command: `usethis::use_pkgdown_github_page`;
@@ -25,7 +51,7 @@
     -  p.value: p-value of the t-test.
     -  data.name: description of data.
 
-### Changes
+### Methods Altered
 -  `corr_fun`: Now uses C++ while using distance correlation.
 
 ## 0.3.0

R/acca.R

@@ -1,6 +1,7 @@
 #' @useDynLib corrp, .registration=TRUE
 #' @importFrom Rcpp evalCpp
 #' @importFrom RcppArmadillo armadillo_version
+#' @importFrom corrplot corrplot
 
 #' @title Average correlation clustering algorithm
 #'
@@ -16,13 +17,13 @@
 #' @param maxrep \[\code{integer(1)}]\cr maximum number of
 #' interactions without change in the clusters.
 #' @param maxiter \[\code{integer(1)}]\cr maximum number of interactions.
-#' @param ... Additional arguments (TODO).
+#' @param ... Additional arguments .
 #'
 #' @return \[\code{acca_list(k)}]\cr A list with the
 #' final result of the clustering method.
 #'  That is, the name of the variables belonging to each cluster k.
 #'
-#' @author Igor D.S. Siciliani
+#' @author Igor D.S. Siciliani, Paulo H. dos Santos
 #'
 #' @keywords correlation , acca
 #'
@@ -31,12 +32,18 @@
 #' "Average correlation clustering algorithm (ACCA) for grouping of co-regulated
 #' genes with similar pattern of variation in their expression values."
 #' Journal of Biomedical Informatics 43.4 (2010): 560-568.
+#' 
+#' @examples
 #'
-#'
+#' x <- corrp::corrp(iris)
+#' m <- corrp::corr_matrix(x)
+#' corrp::acca(m, 2)
 #'
 #' @export
 #'
-acca <- function(m, ...) {
+acca <- function(m, k, ...) {
+  assert_required_argument(m, "The 'm' argument must be a cmatrix object, which is the output from corr_matrix function, or it must be a matrix.")
+  assert_required_argument(m, "The 'k' argument must be the number of number of clusters considered.")
   UseMethod("acca", m)
 }
 

R/best_acca.R

@@ -12,15 +12,15 @@
 #' without change in the clusters in the ACCA method.
 #' @param maxiter \[\code{integer(1)}]\cr maximum number
 #' of interactions in the ACCA method.
-#' @param ... Additional arguments (TODO).
+#' @param ... Additional arguments.
 #'
 #' @return \[\code{list(3)}]\cr A list with:
 #' silhouette average with per k `$silhouette.ave`;
 #' the sequence of clusters tested `$k` and
 #' the optimal number of clusters `$best.k`.
 #' @seealso \code{\link{sil_acca}}
 #'
-#' @author Igor D.S. Siciliani
+#' @author Igor D.S. Siciliani, Paulo H. dos Santos
 #'
 #' @keywords silhouette , acca , optimal , k
 #'
@@ -35,11 +35,16 @@
 #' "International Conference on Artificial Intelligence
 #' and Soft Computing. Springer, Cham, 2015.
 #'
+#' @examples
 #'
+#' x <- corrp::corrp(iris)
+#' m <- corrp::corr_matrix(x)
+#' best_acca(m, 2, 6)
 #'
 #' @export
 #'
 best_acca <- function(m, ...) {
+  assert_required_argument(m, "The 'm' argument must be a cmatrix object, which is the output from corr_matrix function, or it must be a matrix.")
   UseMethod("best_acca", m)
 }