Deploying to gh-pages from @ d760fca 🚀

Author: smwindecker

articles/algorithmic-scaling.html

@@ -303,10 +303,10 @@ knitr::kable(scaling_results,
 
 | method      | pathogen_structure | scaling_exponent | r_squared |
 |:------------|:-------------------|-----------------:|----------:|
-| p_spline    | multiple           |            1.013 |     0.996 |
-| p_spline    | single             |            0.842 |     0.989 |
-| random_walk | multiple           |            0.955 |     0.999 |
-| random_walk | single             |            0.885 |     0.983 |
+| p_spline    | multiple           |            1.004 |     0.996 |
+| p_spline    | single             |            0.825 |     0.991 |
+| random_walk | multiple           |            0.956 |     0.999 |
+| random_walk | single             |            0.858 |     0.981 |
 
 Scaling exponents: time complexity approximately O(n^exponent) {.table}
 
@@ -852,7 +852,7 @@ sessionInfo()
 #> 
 #> loaded via a namespace (and not attached):
 #>  [1] tidyselect_1.2.1    viridisLite_0.4.3   timeDate_4052.112  
-#>  [4] farver_2.1.2        viridis_0.6.5       loo_2.10.0         
+#>  [4] farver_2.1.2        viridis_0.6.5       loo_2.10.1         
 #>  [7] S7_0.2.2            fastmap_1.2.0       digest_0.6.39      
 #> [10] rpart_4.1.27        timechange_0.4.0    lifecycle_1.0.5    
 #> [13] StanHeaders_2.32.10 survival_3.8-6      magrittr_2.0.5     

articles/algorithmic-scaling.md

@@ -818,7 +818,7 @@ sessionInfo()
 #> 
 #> loaded via a namespace (and not attached):
 #>  [1] tidyselect_1.2.1    viridisLite_0.4.3   timeDate_4052.112  
-#>  [4] farver_2.1.2        viridis_0.6.5       loo_2.10.0         
+#>  [4] farver_2.1.2        viridis_0.6.5       loo_2.10.1         
 #>  [7] S7_0.2.2            fastmap_1.2.0       digest_0.6.39      
 #> [10] rpart_4.1.27        timechange_0.4.0    lifecycle_1.0.5    
 #> [13] StanHeaders_2.32.10 survival_3.8-6      magrittr_2.0.5     

articles/algorithmic-scaling_files/figure-html/plot-scaling-1.png

@@ -26,10 +26,14 @@
   `%||%` from `rlang` instead of relying on base R’s version, which only
   exists from R 4.4.0 (related to
   [\#43](https://github.com/acefa-hubs/EpiStrainDynamics/issues/43)).
-- Fixed intermittent R CMD check failures on Windows CI, where compiling
-  the six bundled Stan models exhausted the runner’s default virtual
-  memory (pagefile) at an inconsistent point in the build, by enlarging
-  the pagefile on the Windows job.
+- Fixed intermittent R CMD check failures on Windows CI (“cc1plus.exe:
+  out of memory” / “Build process failed”), caused by Rtools compiling
+  the six bundled Stan models’ heavy Eigen/Boost/StanHeaders template
+  instantiations in parallel and exceeding the runner’s available
+  memory, by forcing serial compilation (`MAKEFLAGS=-j1`) and lowering
+  optimisation to `-O1` for Windows specifically via a new
+  `src/Makevars.win`. Also enlarged the Windows runner’s pagefile as an
+  additional safeguard.
 
 ### Minor improvements
 

articles/parameter-recovery.html

@@ -5,7 +5,7 @@ articles:
   articles/algorithmic-scaling: algorithmic-scaling.html
   articles/parameter-recovery: parameter-recovery.html
   Using-EpiStrainDynamics: Using-EpiStrainDynamics.html
-last_built: 2026-07-24T12:36Z
+last_built: 2026-07-27T10:12Z
 urls:
   reference: https://acefa-hubs.github.io/EpiStrainDynamics/reference
   article: https://acefa-hubs.github.io/EpiStrainDynamics/articles