some little changes

DESCRIPTION

@@ -13,7 +13,7 @@ Authors@R: c( person("Stavros", "Stavroglou", role = c("aut"),
                      comment = c(ORCID = "0009-0006-0095-0243")))
 Maintainer: Hui Wang <[email protected]>
 Description: The model proposes a robust methodology for detecting and reconstructing the hidden structure of dynamic complex systems through short-term forecasts and information embedded in reconstructed state spaces. The approach not only identifies critical components and causal interactions within these systems but also provides a practical tool for optimizing system performance and stability.
-License: MIT + file LICENSE
+License: GPL-3 | file LICENSE
 Depends: R (>= 4.1.0)
 Imports: 
     stats,
@@ -28,7 +28,8 @@ Suggests:
     rmarkdown,
     stringr,
     ggplot2,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    lintr
 Config/Needs/website:
     tidyverse/tidytemplate
 URL: https://github.com/skstavroglou/pattern_causality/

LICENSE

@@ -1,2 +1,17 @@
-YEAR: 2024
-COPYRIGHT HOLDER: Stavros Stavroglou
+GNU GENERAL PUBLIC LICENSE
+Version 3, 29 June 2007
+
+Copyright (C) 2024 Stavros Stavroglou
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.

NEWS.md

@@ -0,0 +1,12 @@
+# patterncausality 0.1.3
+
+* Added cross validation function for pattern causality
+* Improved documentation and vignettes
+* Fixed bugs in parameter optimization
+* Added new plotting functions
+
+# patterncausality 0.1.2
+
+* Initial CRAN release
+* Implemented core pattern causality algorithm
+* Added basic visualization tools

README.md

@@ -189,3 +189,14 @@ Monash Business School and is the author and maintainer of the
 - Stavroglou, S. K., Ayyub, B. M., Kallinterakis, V., Pantelous, A. A.,
   & Stanley, H. E. (2021). A novel causal risk‐based decision‐making
   methodology: The case of coronavirus. _Risk Analysis, 41(5)_, 814-830.
+
+## Test environments
+* local R installation, R 4.1.0
+* ubuntu 20.04 (on GitHub Actions), R 4.1.0
+* win-builder (devel)
+
+## R CMD check results
+0 errors | 0 warnings | 0 notes
+
+## Downstream dependencies
+There are currently no downstream dependencies for this package

inst/CONTRIBUTING.md

@@ -0,0 +1,31 @@
+# Contributing to patterncausality
+
+Thank you for your interest in contributing to patterncausality! 
+
+## How to contribute
+
+1. Fork the repository
+2. Create a new branch for your feature
+3. Make your changes
+4. Add tests for new functionality
+5. Run `devtools::check()`
+6. Submit a pull request
+
+## Code style
+
+* Follow the tidyverse style guide
+* Use roxygen2 for documentation
+* Add examples to function documentation
+* Keep functions focused and modular
+
+## Testing
+
+* Add tests for new functions
+* Ensure all tests pass locally
+* Maintain or improve code coverage
+
+## Documentation
+
+* Update vignettes if needed
+* Keep README.md current
+* Document all exported functions

tests/testthat.R

@@ -0,0 +1,4 @@
+library(testthat)
+library(patterncausality)
+
+test_check("patterncausality")

tests/testthat/test-pcLightweight.R

@@ -0,0 +1,14 @@
+test_that("pcLightweight works", {
+  data(climate_indices)
+  X <- climate_indices$AO
+  Y <- climate_indices$AAO
+
+  result <- pcLightweight(X, Y, E = 3, tau = 2, 
+                         metric = "euclidean", h = 1, 
+                         weighted = TRUE, tpb = FALSE)
+
+  expect_type(result, "list")
+  expect_named(result, c("total", "positive", "negative", "dark"))
+  expect_true(all(sapply(result, is.numeric)))
+  expect_true(all(sapply(result, function(x) x >= 0 && x <= 1)))
+})