Merge pull request #550 from aloctavodia/r210

Bump release

Author: aloctavodia

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: projpred
 Encoding: UTF-8
 Title: Projection Predictive Feature Selection
-Version: 2.9.1.9001
-Date: 2025-11-02
+Version: 2.10.0
+Date: 2025-12-05
 Authors@R: c(person("Juho", "Piironen", role = c("aut"),
                     email = "[email protected]"),
              person("Markus", "Paasiniemi", role = "aut"),

NEWS.md

@@ -2,13 +2,15 @@
 
 If you read this from a place other than <https://mc-stan.org/projpred/news/index.html>, please consider switching to that website since it features better formatting and cross-linking.
 
-# projpred 2.9.1.9000 (development)
+# projpred 2.10.0
 
 ## Major changes
 
 * Added support for censored observations when using the latent projection (with response-scale analyses). This makes it possible, e.g., to use the latent projection for time-to-event models (also known as models for survival analysis). Due to this new feature, the function passed to argument `latent_ll_oscale` of `extend_family()` now needs to have an argument `cens`. See `?extend_family` (section "Latent projection") as well as the latent-projection vignette (section ["Censored observations (survival analysis)"](https://mc-stan.org/projpred/articles/latent.html#cens)) for more information and examples. Note that only the performance statistics `"elpd"`, `"mlpd"`, and `"gmpd"` take censoring into account (on response scale). (GitHub: #528)
 
 ## Minor changes
+
+* `suggest_size()` returns `nterms_max` instead of NA when no model satisfies the criterion
 * Use `reformulas` package directly for formula processing functions. This package is already a dependency of `lme4` >= v1.1-38.
 
 ## Bug fixes

cran-comments.md

@@ -1,12 +1,13 @@
 ## Test environments
 
 * Local:
-    + R version 4.5.1 (2025-06-13) on Ubuntu 25.04 system (platform:
+    + R version 4.5.1 (2025-06-13) on Ubuntu 24.04.3 LTS system (platform:
       x86_64-pc-linux-gnu (64-bit))
 * win-builder:
-    + R-devel (R Under development (unstable) (2025-07-02 r88374 ucrt))
-    + R-release (R version 4.5.1 (2025-06-13 ucrt))
-    + R-oldrelease (R version 4.4.3 (2025-02-28 ucrt))
+    + R-devel R Under development (unstable) (2025-12-04 r89100 ucrt)
+    + R-release (R version 4.5.2 (2025-10-31 ucrt))
+    + R-oldrelease (version 4.4.3 (2025-02-28 ucrt))
+
 
 ## R CMD check results
 
@@ -16,76 +17,23 @@ All checks gave neither ERRORs nor WARNINGs.
 
 The local check on a Linux system gave the following NOTEs:
 
-    * checking CRAN incoming feasibility ... [10s/60s] NOTE
-    Maintainer: ‘Osvaldo Martin <[e-mail address]>’
-    
-    New maintainer:
-      Osvaldo Martin <[e-mail address]>
-    Old maintainer(s):
-      Frank Weber <[e-mail address]>
-    
     Suggests or Enhances not in mainstream repositories:
       cmdstanr
     Availability using Additional_repositories specification:
       cmdstanr   yes   https://stan-dev.r-universe.dev/
 
-    Found the following (possibly) invalid URLs:
-      URL: https://sites.stat.columbia.edu/gelman/arm/
-        From: man/mesquite.Rd
-        Status: Error
-        Message: libcurl error code 60:
-          	SSL certificate problem: unable to get local issuer certificate
-          	(Status without verification: OK)
-      URL: https://sites.stat.columbia.edu/gelman/arm/examples/mesquite/mesquite.dat
-        From: man/mesquite.Rd
-        Status: Error
-        Message: libcurl error code 60:
-          	SSL certificate problem: unable to get local issuer certificate
-          	(Status without verification: OK)
-    
-    * checking compilation flags used ... NOTE
-    Compilation used the following non-portable flag(s):
-      ‘-mno-omit-leaf-frame-pointer’
-    
-    * checking examples ... [27s/28s] NOTE
-    Examples with CPU (user + system) or elapsed time > 5s
-                          user system elapsed
-    as.matrix.projection 8.788  0.437   9.376
-
-As stated in the first NOTE, we would like to change the maintainer in this
-release.
-
-As also stated in the first NOTE, the 'cmdstanr' package
+As stated in the first NOTE, the 'cmdstanr' package
 (<https://mc-stan.org/cmdstanr/>) is not available on CRAN. The 'cmdstanr'
 backend can be used in 'projpred''s unit tests, but it is not necessary for
 'projpred' to work. As this NOTE says, we have added the repository URL for the
 'cmdstanr' package to the 'DESCRIPTION' file (field 'Additional_repositories').
 
-The URLs reported as possibly invalid in the first NOTE are in fact accessible.
-The certificate problems are not related to 'projpred'.
-
-The compilation flag reported in the second NOTE is not set within 'projpred',
-so it is probably due to the system that this local check ran on. In CRAN
-checks, this NOTE has never appeared yet (but it is shown when checking the
-previous CRAN version 2.8.0 locally).
-
-The runtime of the 'as.matrix.projection' example (see the third NOTE) may
-sometimes be slightly > 5s.
-
 ### win-builder checks
 
 #### R-devel
 
 The R-devel check on win-builder gave the following NOTE:
-    
-    * checking CRAN incoming feasibility ... [15s] NOTE
-    Maintainer: 'Osvaldo Martin <[e-mail address]>'
-    
-    New maintainer:
-      Osvaldo Martin <[e-mail address]>
-    Old maintainer(s):
-      Frank Weber <[e-mail address]>
-    
+        
     Suggests or Enhances not in mainstream repositories:
       cmdstanr
     Availability using Additional_repositories specification:
@@ -97,14 +45,6 @@ For an explanation of this NOTE, see the explanations for the local check above.
 
 The R-release check on win-builder gave the following NOTEs:
 
-    * checking CRAN incoming feasibility ... [14s] NOTE
-    Maintainer: 'Osvaldo Martin <[e-mail address]>'
-    
-    New maintainer:
-      Osvaldo Martin <[e-mail address]>
-    Old maintainer(s):
-      Frank Weber <[e-mail address]>
-    
     Suggests or Enhances not in mainstream repositories:
       cmdstanr
     Availability using Additional_repositories specification:
@@ -115,20 +55,13 @@ For an explanation of this NOTE, see the explanations for the local check above.
 #### R-oldrelease
 
 The R-oldrelease check on win-builder gave the following NOTEs:
-    
-    * checking CRAN incoming feasibility ... [20s] NOTE
-    Maintainer: 'Osvaldo Martin <[e-mail address]>'
-    
-    New maintainer:
-      Osvaldo Martin <[e-mail address]>
-    Old maintainer(s):
-      Frank Weber <[e-mail address]>
+
 
     Suggests or Enhances not in mainstream repositories:
       cmdstanr
     Availability using Additional_repositories specification:
       cmdstanr   yes   https://stan-dev.r-universe.dev/
-    
+
     * checking package dependencies ... NOTE
     Packages suggested but not available for checking: 'unix', 'cmdstanr'
 

vignettes/projpred.Rmd

@@ -81,7 +81,7 @@ tau0 <- p0 / (D - p0) * 1 / sqrt(N)
 We now fit the reference model to the data.
 To make this vignette build faster, we use only 2 MCMC chains and 1000 iterations per chain (with half of them being discarded as warmup draws).
 In practice, 4 chains and 2000 iterations per chain are reasonable defaults.
-Furthermore, we make use of [**rstan**](https://mc-stan.org/rstan/)'s parallelization, which means to run each chain on a separate CPU core^[More generally, the number of chains is split up as evenly as possible among the number of CPU cores.].
+Furthermore, we make use of [**rstan**](https://mc-stan.org/)'s parallelization, which means to run each chain on a separate CPU core^[More generally, the number of chains is split up as evenly as possible among the number of CPU cores.].
 If you run the following code yourself, you can either rely on an automatic mechanism to detect the number of CPU cores (like the `parallel::detectCores()` function shown below) or adapt `ncores` manually to your system.
 ```{r ref_fit}
 # Set this manually if desired: