Reinstate disabled tables

[ns-rse]

In fixing the method used in imputation for some unknown reason as yet unresolved many of the gtsummary::tbl_summary() tables such were causing errors on rendering the document.

Error occurs after processing everyting to index.knit.md...

128/130 [xgboost-save]                                      
129/130 [tbl-variables]                                     
130/130                                                     
output file: index.knit.md

Rendering qmd embeds [index.qmd]
Error running filter /home/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:
Inline, list of Inlines, or string expected, got Blocks
	while retrieving function argument content
	while retrieving arguments for function Plain
stack traceback:
	...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:16561: in function <...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:16387>
	(...tail calls...)
	...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:2947: in function <...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:2941>
	(...tail calls...)
	[C]: in ?
	[C]: in method 'walk'
	...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:557: in function <...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:546>
	(...tail calls...)
	...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:1334: in local 'callback'
	...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:1352: in upvalue 'run_emulated_filter_chain'
	...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:1388: in function <...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:1385>
stack traceback:
	...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:557: in function <...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:546>
	(...tail calls...)
	...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:1334: in local 'callback'
	...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:1352: in upvalue 'run_emulated_filter_chain'
	...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:1388: in function <...e/neil/.local/quarto/quarto-1.6.3/share/filters/main.lua:1385>

Affected tables are (these are the label: for each code chunk...

• tbl-patient-demographics
• tbl-clinical-characteristics
• tbl-biomarkers-variables
• tbl-ultrasound-characteristics
• tbl-u-class-final-path
• tbl-thy-class-final-path
• tbl-cytology-characteristics
• tbl-data-completness - this may be redundant though as there is a fair bit of duplication with tbl-predictors and much of the information is in the tbl-imputation-summary-[pmm|cart|rf] tables.
• tbl-predictors - see above comment.

These have therefore been disabled by setting eval: false but some may need reinstating/fixing.

This may be related to a recent update to gtsummary-1.7.2 (2024-07-15) which is showing on CRAN as broken and in need of fixing.

There is active work on-going in the gtsummary repository as they work towards v2.0.0 release so we may see this addressed in due course. I haven't (yet) raised an issue as a) its the weekend and b) I've not been able to recreate a minimal reproducible example to demonstrate the problem.