Error(s) in re-building vignettes:
--- re-building 'all_tables_examples.Rmd' using rmarkdown

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(obstruct.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(extent.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, extent.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(obstruct.factor, extent.factor) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(age.factor, mort_5yr) :
  Chi-squared approximation may be incorrect
Warning in chisq.test(obstruct.factor, mort_5yr) :
  Chi-squared approximation may be incorrect
Note: dependent includes missing data. These are dropped.
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Note: dependent includes missing data. These are dropped.
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Setting levels: control = 0, case = 1
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Setting levels: control = 0, case = 1
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Setting levels: control = 0, case = 1
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boundary (singular) fit: see ?isSingular
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Note: dependent includes missing data. These are dropped.
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P-value for lmer is estimate assuming t-distribution is normal. Bootstrap for final publication.
Note: dependent includes missing data. These are dropped.
boundary (singular) fit: see ?isSingular
P-value for lmer is estimate assuming t-distribution is normal. Bootstrap for final publication.
Note: dependent includes missing data. These are dropped.
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Dependent variable is a survival object
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

The following object is masked from 'package:graphics':

    dotchart

--- finished re-building 'all_tables_examples.Rmd'

--- re-building 'bootstrap.Rmd' using rmarkdown
--- finished re-building 'bootstrap.Rmd'

--- re-building 'data_prep.Rmd' using rmarkdown
--- finished re-building 'data_prep.Rmd'

--- re-building 'export.Rmd' using rmarkdown
Note: dependent includes missing data. These are dropped.
Warning in chisq.test(extent.factor, differ.factor) :
  Chi-squared approximation may be incorrect
Note: dependent includes missing data. These are dropped.
Warning in chisq.test(extent.factor, differ.factor) :
  Chi-squared approximation may be incorrect
Note: dependent includes missing data. These are dropped.
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--- finished re-building 'export.Rmd'

--- re-building 'finalfit.Rmd' using rmarkdown
Warning in chisq.test(age.factor, perfor.factor) :
  Chi-squared approximation may be incorrect
Note: dependent includes missing data. These are dropped.
Note: dependent includes missing data. These are dropped.
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Setting levels: control = 0, case = 1
Setting direction: controls < cases
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--- finished re-building 'finalfit.Rmd'

--- re-building 'missing.Rmd' using rmarkdown

Attaching package: 'mice'

The following object is masked from 'package:stats':

    filter

The following objects are masked from 'package:base':

    cbind, rbind

Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Setting levels: control = 0, case = 1
Setting direction: controls < cases
Note: dependent includes missing data. These are dropped.
Warning: Removed 3 rows containing missing values (geom_errorbarh).
Note: dependent includes missing data. These are dropped.
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--- finished re-building 'missing.Rmd'

--- re-building 'survival.Rmd' using rmarkdown
Quitting from lines 153-158 (survival.Rmd) 
Error: processing vignette 'survival.Rmd' failed with diagnostics:
there is no package called 'survminer'
--- failed re-building 'survival.Rmd'

SUMMARY: processing the following file failed:
  'survival.Rmd'

Error: Vignette re-building failed.
Execution halted