Develop

.Rbuildignore

@@ -13,9 +13,11 @@
 ^\.rtms-instructions\.md$
 ^\.vscode$
 ^cran-comments\.md$
+^LICENSE\.md$
 ^data-raw$
 ^dev$
 ^docs$
+^specs$
 ^AGENTS\.md$
 ^NEWS\.md$
 ^pkgdown$

.github/CONTRIBUTING.md

@@ -9,11 +9,14 @@ Thank you for your interest in contributing to **rtemis**! This guide will help
 Ensure you're using the latest version of rtemis (v0.99+). Many issues may already be fixed in recent updates.
 
 ```r
-# Update from GitHub
-pak::pkg_install("rtemis-org/rtemis")
+# Install from CRAN
+install.packages("rtemis")
 
-# Or from r-universe
-install.packages('rtemis', repos = 'https://egenn.r-universe.dev')
+# Install from GitHub
+pak::pak("rtemis-org/rtemis")
+
+# Install from r-universe
+install.packages('rtemis', repos = 'https://rtemis-org.r-universe.dev')
 
 # Check your version
 packageVersion("rtemis")
@@ -25,9 +28,8 @@ Please search [existing issues](https://github.com/rtemis-org/rtemis/issues) to
 
 ### Review Documentation
 
-- **API Documentation**: https://rdocs.rtemis.org/api/
-- **General Documentation**: https://rdocs.rtemis.org
-- **Copilot Instructions**: `.github/copilot-instructions.md` (for developers)
+- **API Documentation**: https://docs.rtemis.org/r/ml-api/
+- **General Documentation**: https://docs.rtemis.org/r/ml
 
 ## Opening an Issue
 
@@ -159,8 +161,6 @@ While this guide focuses on issues, pull requests are welcome! Key points:
 - Include tests for new functionality
 - Update documentation as needed
 
-See `.github/copilot-instructions.md` for detailed coding conventions.
-
 ## Questions?
 
 - **General usage**: [GitHub Discussions](https://github.com/rtemis-org/rtemis/discussions)

.gitignore

@@ -3,6 +3,7 @@ __dev/
 __validation/
 dev/
 __out/
+specs/
 
 # Mac OS
 .DS_Store

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: rtemis
 Version: 1.0.1
 Title: Machine Learning and Visualization
-Date: 2026-04-03
+Date: 2026-04-20
 Authors@R: person(given = "E.D.", family = "Gennatas", role = c("aut", "cre", "cph"), 
     email = "gennatas@gmail.com", comment = c(ORCID = "0000-0001-9280-3609"))
 Description: Machine learning and visualization package with an 'S7' backend 
@@ -13,7 +13,7 @@ Description: Machine learning and visualization package with an 'S7' backend
     execution, and interactive visualizations. The package first appeared in E.D. Gennatas (2017)
     <https://repository.upenn.edu/entities/publication/d81892ea-3087-4b71-a6f5-739c58626d64>.
 License: GPL (>= 3)
-URL: https://www.rtemis.org, https://docs.rtemis.org/r/, https://docs.rtemis.org/r-api/
+URL: https://www.rtemis.org, https://docs.rtemis.org/r/ml, https://docs.rtemis.org/r/ml-api/
 BugReports: https://github.com/rtemis-org/rtemis/issues
 ByteCompile: yes
 Depends:

NEWS.md

@@ -0,0 +1,9 @@
+# rtemis news
+
+## 1.0.0 First CRAN release
+
+## 1.0.1
+
+- Introduce `VariableImportance` S7 class to represent variable importance data, allowing for more than one measure of importance per model and update all relevant classes and methods.
+- Calculate Partial_Effect_Variance as variable importance measure for GAM models
+- Add `execution_config` argument to internal `train_` method and use it in LightRuleFit to propagate to LightGBM and GLMNET calls.

R/rtemis-package.R

@@ -8,7 +8,7 @@
 #' Advanced Machine Learning & Visualization made efficient, accessible, reproducible
 #'
 #' @section Online Documentation and Vignettes:
-#' <https://docs.rtemis.org/r/>
+#' <https://docs.rtemis.org/r/ml>
 #'
 #' @section System Setup:
 #' There are some options you can define in your .Rprofile (usually found in your home directory),

R/zzz.R

@@ -89,7 +89,7 @@ setup_progress <- function() {
       bold("\n  Resources"),
       "\n  \u2502    ",
       gray("Docs:"),
-      " https://docs.rtemis.org/r/",
+      " https://docs.rtemis.org/r/ml",
       "\n  \u2502 ",
       gray("Learn R:"),
       " https://pdsr.rtemis.org",

README.md

@@ -4,7 +4,7 @@
 
 # rtemis: Advanced Machine Learning & Visualization.
 
-[![rtemis cover](https://docs.rtemis.org/r/assets/docs-cover.avif)](https://docs.rtemis.org/r/)
+[![rtemis cover](https://docs.rtemis.org/r/ml/assets/docs-cover.avif)](https://docs.rtemis.org/r/ml/)
 
 This is the new version of the rtemis R package and remains under active development.
 
@@ -148,7 +148,7 @@ The new release includes the `draw` family of functions, the evolution of the `d
 
 ## Documentation
 
-The documentation is available at [docs.rtemis.org/r](https://docs.rtemis.org/r/), which includes
+The documentation is available at [docs.rtemis.org/r/ml](https://docs.rtemis.org/r/ml), which includes
 walkthroughs of main features and full API reference.
 
 ## Ongoing work
@@ -158,3 +158,8 @@ There is a lot more coming - both within this package and the other packages in
 ## rtemisalpha
 
 The original, unmaintained version of rtemis remains available as `rtemisalpha` at [rtemis-org/rtemis-legacy](https://github.com/rtemis-org/rtemis-legacy).
+
+---
+
+© 2016–2026 E.D. Gennatas. Licensed under [GPL (>= 3)](https://www.gnu.org/licenses/gpl-3.0.html).
+

tests/testthat/test_Supervised.R

@@ -1363,9 +1363,3 @@ test_that("train() with preprocessor creates a model with the preprocessor", {
   expect_s7_class(mod_c_glm_pp, Classification)
   expect_true(!is.null(mod_c_glm_pp@preprocessor))
 })
-
-# %% GAM univariate
-x <- rnorm(500)
-x2 <- rnorm(500)
-y <- x^3 + rnorm(500)
-mod <- train(data.table(x, x2, y), algorithm = "gam")