Fix fev1 vignette

openpharma · May 31, 2024 · 1266a53 · 1266a53
1 parent fbbbf66
commit 1266a53
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Showing 8 changed files with 152 additions and 157 deletions.
diff --git a/vignettes/archetypes.Rmd.upstream → vignettes/archetypes.Rmd.source b/vignettes/archetypes.Rmd.upstream → vignettes/archetypes.Rmd.source
diff --git a/vignettes/bcva.Rmd.upstream → vignettes/bcva.Rmd.source b/vignettes/bcva.Rmd.upstream → vignettes/bcva.Rmd.source
@@ -258,7 +258,7 @@ for (level in visit_levels) {
 b_mmrm_summary <- b_mmrm_draws |>
   summarize_draws() |>
   select(variable, mean, sd) |>
-  filter(!(variable %in% c("lprior", "lp__"))) |>
+  filter(!(variable %in% c("Intercept", "lprior", "lp__"))) |>
   rename(bayes_estimate = mean, bayes_se = sd) |>
   mutate(
     variable = variable |>

diff --git a/vignettes/fev1.Rmd b/vignettes/fev1.Rmd
diff --git a/vignettes/fev1.Rmd.upstream → vignettes/fev1.Rmd.source b/vignettes/fev1.Rmd.upstream → vignettes/fev1.Rmd.source
@@ -1,6 +1,6 @@
 ---
 title: FEV1 data comparison between Bayesian and frequentist MMRMs
-date: "`r format(Sys.time(), '%d/%m/%Y')`"
+date: "`r format(Sys.time(), '%Y-%d-%m')`"
 output:
   rmarkdown::html_document:
     theme: spacelab
@@ -269,7 +269,7 @@ for (level in visit_levels) {
 b_mmrm_summary <- b_mmrm_draws |>
   summarize_draws() |>
   select(variable, mean, sd) |>
-  filter(!(variable %in% c("lprior", "lp__"))) |>
+  filter(!(variable %in% c("Intercept", "lprior", "lp__"))) |>
   rename(bayes_estimate = mean, bayes_se = sd) |>
   mutate(
     variable = variable |>
@@ -399,3 +399,9 @@ gt(table_se) |>
     diff_relative_se = "Relative"
   )
 ```
+
+## Session info {#session}
+
+```{r}
+sessionInfo()
+```
diff --git a/vignettes/simulation.Rmd.upstream → vignettes/simulation.Rmd.source b/vignettes/simulation.Rmd.upstream → vignettes/simulation.Rmd.source
diff --git a/vignettes/subgroup.Rmd b/vignettes/subgroup.Rmd
@@ -1,7 +1,7 @@
 ---
 title: "Subgroup analysis"
-bibliography: '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/brms.mmrm/bibliography.bib'
-csl: '/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/brms.mmrm/asa.csl'
+bibliography: '`r system.file("bibliography.bib", package = "brms.mmrm")`'
+csl: '`r system.file("asa.csl", package = "brms.mmrm")`'
 output:
   rmarkdown::html_vignette:
     toc: true

diff --git a/vignettes/subgroup.Rmd.upstream → vignettes/subgroup.Rmd.source b/vignettes/subgroup.Rmd.upstream → vignettes/subgroup.Rmd.source
diff --git a/vignettes/usage.Rmd.upstream → vignettes/usage.Rmd.source b/vignettes/usage.Rmd.upstream → vignettes/usage.Rmd.source