Merge pull request #5 from kapsner/main

merge latest upstream changes

Author: kapsner

.Rbuildignore

@@ -12,3 +12,5 @@ LICENSE
 ^misc$
 ^cran-comments\.md$
 ^vignettes/articles$
+^tests$
+^CRAN-SUBMISSION$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: survex
 Title: Explainable Machine Learning in Survival Analysis
-Version: 1.1.1.9001
+Version: 1.1.3.9001
 Authors@R: 
     c(
         person("Mikołaj", "Spytek", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7111-2286")),

NEWS.md

@@ -1,4 +1,4 @@
-# survex 1.1.0
+# survex 1.1.3
 
 * fixed not being able to plot or print SurvLIME results for the cph model sometimes. ([#72](https://github.com/ModelOriented/survex/issues/72))
 * added global explanations via the SurvSHAP(t) method (see `model_survshap()` function)

README.md

@@ -20,12 +20,6 @@ Note that an explainer can be created for **any** survival model, using the `exp
 
 ## Installation
 
-```diff
-! Please note that that version v1.1.1 with new functionalities is still being processed by CRAN.
-+ To use all functionalities, for the time being, please install the most current version from GitHub!
-```
-
-
 The package is available on [CRAN](https://cran.r-project.org/package=survex):
 
 ```r
@@ -107,6 +101,7 @@ If you use `survex`, please cite [our preprint](https://arxiv.org/abs/2308.16113
 - H. Baniecki, B. Sobieski, P. Bombiński, P. Szatkowski, P. Biecek. [Hospital Length of Stay Prediction Based on Multi-modal Data towards Trustworthy Human-AI Collaboration in Radiomics](https://arxiv.org/abs/2303.09817). *International Conference on Artificial Intelligence in Medicine*, 2023.
 - W. Chen, B. Zhou, C. Y. Jeon, F. Xie, Y-C. Lin, R. K. Butler, Y. Zhou, T. Q. Luong, E. Lustigova, J. R. Pisegna, B. U. Wu. [Machine learning versus regression for prediction of sporadic pancreatic cancer](https://doi.org/10.1016/j.pan.2023.04.009). *Pancreatology*, 2023.
 - M. Nachit, Y. Horsmans, R. M. Summers, I. A. Leclercq, P. J. Pickhardt. [AI-based CT Body Composition Identifies Myosteatosis as Key Mortality Predictor in Asymptomatic Adults](https://doi.org/10.1148/radiol.222008). *Radiology*, 2023.
+- R. Passera, S. Zompi, J. Gill, A. Busca. [Explainable Machine Learning (XAI) for Survival in Bone Marrow Transplantation Trials: A Technical Report](https://doi.org/10.3390/biomedinformatics3030048). *BioMedInformatics*, 2023.
 - Share it with us!
 
 ## Related work

cran-comments.md

@@ -1,25 +1,10 @@
-## Resubmission 30/08/2023 v.1.1.1
+## Resubmission  05/09/2023 v.1.1.3
 
 * Fix notes about long running examples by wrapping
   in \donttest{} blocks.
-* Previous submission (v.1.1.0) also had the following
-  notes from `r-devel-linux-x86_64-debian-gcc` flavor
-  check:
-    - Running R code in 'testthat.R' had CPU time
-      7.6 times elapsed time
-    - Re-building vignettes had CPU time
-      10.8 times elapsed time
-  I could not replicate these in any other environment:
-    - locally using R CMD Check (Windows),
-    - on r_hub (Windows, macos, and linux)
-    - using R CMD Check in GitHub Actions runners
-      (Windows, Ubuntu, macos)
-    - using `devtools::check_win_devel()` and
-      `check_macos_release()`
-  I believe these to be false positives likely due to
-  hardware or current load at the time of the check
-  in case they are not, please provide advice how to fix.
-
+* Fix notes about CPU time being much longer than elapsed
+  time when running tests and building vignettes.
+  
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note