quarto monkeying around

.gitignore

@@ -86,4 +86,5 @@ renv/staging/
 
 # folders to ignore
 data
-data-raw
+data-raw
+analysis/report/.quarto

R/_load_packages.R

@@ -28,6 +28,10 @@ library(cowplot)
 library(ggsurvfit)
 library(plotly)
 
+library(knitr)
+library(quarto)
+library(rmarkdown)
+
 library(gt)
 library(gtsummary)
 library(flextable)

main.R

@@ -20,7 +20,7 @@ source(here('analysis', 'script', 'create_neoadj_dat.R'))
 source(here('analysis', 'script', 'derive_lines_of_therapy.R'))
 rmarkdown::render(
   input = here('analysis', 'report', 'genie-bpc-bladder-clinical.rmd'),
-  output_file = 'genie-bpc-bladder-01-clinical.html',
+  output_file = '01-genie-bpc-bladder-clinical.html',
   output_dir = here('output', 'report')
 )
 
@@ -36,11 +36,22 @@ source(here('analysis', 'script', 'create_gene_panel_dat.R'))
 source(here('analysis', 'script', 'process_oncokb_output.R'))
 rmarkdown::render(
   input = here('analysis', 'report', 'genie-bpc-bladder-genomic.rmd'),
-  output_file = 'genie-bpc-bladder-02-genomic.html',
+  output_file = '02-genie-bpc-bladder-genomic.html',
   output_dir = here('output', 'report')
 )
 
 
 #############################
 # Met classification report #
-#############################
+#############################
+# I cannot get this to render using quarto_render(), frustrating.
+# Do:
+# 1. render analysis/report/genie-bpc-met-class.qmd.
+# 2. Run the following copy command:
+fs::file_move(
+  path = here('analysis', 'report', 'genie-bpc-bladder-met-class.html'),
+  new_path = here('output', 'report', '99-genie-bpc-bladder-met_class.html'),
+  over
+)
+
+

todo.md

@@ -3,6 +3,7 @@
 - Update metastatic classification
 - Update the reports to have better met classification.
 - Review the swimmer plot for errors.
+- Perioperative update?
 - remove repeats in the tables if not already done.
 - add a note to have people review the equivalence classes with carbo and cis in the regimen
 - Send the following to the group: