diff --git a/.Rbuildignore b/.Rbuildignore index 93ad0be7..18303067 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -12,3 +12,5 @@ LICENSE ^misc$ ^cran-comments\.md$ ^vignettes/articles$ +^tests$ +^CRAN-SUBMISSION$ diff --git a/DESCRIPTION b/DESCRIPTION index 900a0765..ad1c5bef 100644 --- a/DESCRIPTION +++ b/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 = "mikolajspytek@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7111-2286")), diff --git a/NEWS.md b/NEWS.md index 50fe2f85..2543d45d 100644 --- a/NEWS.md +++ b/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) diff --git a/README.md b/README.md index d4a74024..1f79c367 100644 --- a/README.md +++ b/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 diff --git a/cran-comments.md b/cran-comments.md index 4d49d008..167790c5 100644 --- a/cran-comments.md +++ b/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 diff --git a/misc/cen_slides.pdf b/misc/cen_slides.pdf new file mode 100644 index 00000000..a95b3506 Binary files /dev/null and b/misc/cen_slides.pdf differ diff --git a/misc/preprint.pdf b/misc/preprint.pdf new file mode 100644 index 00000000..c6e40882 Binary files /dev/null and b/misc/preprint.pdf differ