shrink vignette size

Genentech · Feb 11, 2025 · fb6b0c4 · fb6b0c4
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diff --git a/vignettes/figure-match_weight_01_methods-unnamed-chunk-28-1.png b/vignettes/figure-match_weight_01_methods-unnamed-chunk-28-1.png
diff --git a/vignettes/figure-match_weight_01_methods-unnamed-chunk-61-1.png b/vignettes/figure-match_weight_01_methods-unnamed-chunk-61-1.png
diff --git a/vignettes/figure-match_weight_01_methods-unnamed-chunk-62-1.png b/vignettes/figure-match_weight_01_methods-unnamed-chunk-62-1.png
diff --git a/vignettes/figure-match_weight_01_methods-unnamed-chunk-67-1.png b/vignettes/figure-match_weight_01_methods-unnamed-chunk-67-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-10-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-10-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-10-2.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-10-2.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-12-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-12-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-19-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-19-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-19-2.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-19-2.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-21-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-21-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-31-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-31-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-32-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-32-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-32-2.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-32-2.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-42-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-42-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-43-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-43-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-44-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-44-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-44-2.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-44-2.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-44-3.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-44-3.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-44-4.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-44-4.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-51-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-51-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-53-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-53-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-60-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-60-1.png
diff --git a/vignettes/figure-match_weight_02_application-unnamed-chunk-62-1.png b/vignettes/figure-match_weight_02_application-unnamed-chunk-62-1.png
diff --git a/vignettes/match_weight_01_methods.Rmd b/vignettes/match_weight_01_methods.Rmd
@@ -4,7 +4,7 @@ bibliography: references.bib
 author: 
   - Manoj Khanal <[email protected]>
   - Eli Lilly & Company
-date: "2025-01-28"
+date: "2025-02-11"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{1. Matching and Weighting Methods}
@@ -105,7 +105,7 @@ trial.data <- rcorrvar2(n = n_t, k_cont = k_cont, k_cat = k_cat, k_nb = 0,
 #> 
 #>  Constants: Distribution  5  
 #> 
-#> Constants calculation time: 0.004 minutes 
+#> Constants calculation time: 0.003 minutes 
 #> Intercorrelation calculation time: 0.002 minutes 
 #> Error loop calculation time: 0 minutes 
 #> Total Simulation time: 0.006 minutes

diff --git a/vignettes/match_weight_02_application.Rmd b/vignettes/match_weight_02_application.Rmd
@@ -4,7 +4,7 @@ bibliography: references.bib
 author: 
   - Manoj Khanal <[email protected]>
   - Eli Lilly & Company
-date: "2025-01-28"
+date: "2025-02-11"
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteIndexEntry{2. Matching and Weighting Application with Dynamic Borrowing}
@@ -341,13 +341,13 @@ results.exp.psborrow<- mcmc_sample(anls_obj,
 )
 #> Running MCMC with 3 sequential chains...
 #> 
-#> Chain 1 finished in 13.6 seconds.
-#> Chain 2 finished in 13.1 seconds.
-#> Chain 3 finished in 12.4 seconds.
+#> Chain 1 finished in 12.7 seconds.
+#> Chain 2 finished in 12.3 seconds.
+#> Chain 3 finished in 12.3 seconds.
 #> 
 #> All 3 chains finished successfully.
-#> Mean chain execution time: 13.0 seconds.
-#> Total execution time: 39.7 seconds.
+#> Mean chain execution time: 12.5 seconds.
+#> Total execution time: 37.7 seconds.
 
 draws1 <- results.exp.psborrow$draws()
 draws1 <- rename_draws_covariates(draws1, anls_obj)
@@ -541,13 +541,13 @@ results.weib.psborrow<- mcmc_sample(anls_obj,
 )
 #> Running MCMC with 3 sequential chains...
 #> 
-#> Chain 1 finished in 28.8 seconds.
-#> Chain 2 finished in 29.4 seconds.
-#> Chain 3 finished in 33.2 seconds.
+#> Chain 1 finished in 29.2 seconds.
+#> Chain 2 finished in 29.3 seconds.
+#> Chain 3 finished in 30.0 seconds.
 #> 
 #> All 3 chains finished successfully.
-#> Mean chain execution time: 30.5 seconds.
-#> Total execution time: 92.2 seconds.
+#> Mean chain execution time: 29.5 seconds.
+#> Total execution time: 89.0 seconds.
 
 draws2 <- results.weib.psborrow$draws()
 draws2 <- rename_draws_covariates(draws2, anls_obj)
@@ -1217,13 +1217,13 @@ results.no.psborrow<- mcmc_sample(anls_obj,
 )
 #> Running MCMC with 3 sequential chains...
 #> 
-#> Chain 1 finished in 3.7 seconds.
-#> Chain 2 finished in 4.1 seconds.
-#> Chain 3 finished in 3.9 seconds.
+#> Chain 1 finished in 3.9 seconds.
+#> Chain 2 finished in 4.2 seconds.
+#> Chain 3 finished in 4.7 seconds.
 #> 
 #> All 3 chains finished successfully.
-#> Mean chain execution time: 3.9 seconds.
-#> Total execution time: 12.1 seconds.
+#> Mean chain execution time: 4.3 seconds.
+#> Total execution time: 13.1 seconds.
 
 draws3 <- results.no.psborrow$draws()
 draws3 <- rename_draws_covariates(draws3, anls_obj)
@@ -1380,13 +1380,13 @@ results.full.psborrow<- mcmc_sample(anls_obj,
 )
 #> Running MCMC with 3 sequential chains...
 #> 
-#> Chain 1 finished in 5.9 seconds.
-#> Chain 2 finished in 5.5 seconds.
-#> Chain 3 finished in 5.9 seconds.
+#> Chain 1 finished in 6.0 seconds.
+#> Chain 2 finished in 5.4 seconds.
+#> Chain 3 finished in 5.4 seconds.
 #> 
 #> All 3 chains finished successfully.
-#> Mean chain execution time: 5.8 seconds.
-#> Total execution time: 17.8 seconds.
+#> Mean chain execution time: 5.6 seconds.
+#> Total execution time: 17.2 seconds.
 
 draws4 <- results.full.psborrow$draws()
 draws4 <- rename_draws_covariates(draws4, anls_obj)

diff --git a/vignettes/original/_match_weight_01_methods.Rmd b/vignettes/original/_match_weight_01_methods.Rmd
@@ -15,7 +15,8 @@ vignette: >
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#>"
+  comment = "#>",
+  dpi = 60
 )
 ```
 

diff --git a/vignettes/original/_match_weight_02_application.Rmd b/vignettes/original/_match_weight_02_application.Rmd
@@ -23,7 +23,8 @@ vignette: >
 ```{r setup, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  comment = "#>"
+  comment = "#>",
+  dpi = 45
 )
 ```