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.
In fixing the
methodused in imputation for some unknown reason as yet unresolved many of thegtsummary::tbl_summary()tables such were causing errors on rendering the document.Error occurs after processing everyting to
index.knit.md...Affected tables are (these are the
label:for each code chunk...tbl-patient-demographicstbl-clinical-characteristicstbl-biomarkers-variablestbl-ultrasound-characteristicstbl-u-class-final-pathtbl-thy-class-final-pathtbl-cytology-characteristicstbl-data-completness- this may be redundant though as there is a fair bit of duplication withtbl-predictorsand much of the information is in thetbl-imputation-summary-[pmm|cart|rf]tables.tbl-predictors- see above comment.These have therefore been disabled by setting
eval: falsebut 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
v2.0.0release 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.