Error(s) in re-building vignettes:
  ...
--- re-building ‘AMR.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

Joining, by = "patient_id"
Warning: Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.
NOTE: Using column `bacteria` as input for `col_mo`.
NOTE: Using column `date` as input for `col_date`.
NOTE: Using column `patient_id` as input for `col_patient_id`.
=> Found 15,842 first weighted isolates (79.2% of total)
Quitting from lines 375-385 (AMR.Rmd) 
Error: processing vignette 'AMR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘AMR.Rmd’

--- re-building ‘EUCAST.Rmd’ using rmarkdown
--- finished re-building ‘EUCAST.Rmd’

--- re-building ‘G_test.Rmd’ using rmarkdown
--- finished re-building ‘G_test.Rmd’

--- re-building ‘SPSS.Rmd’ using rmarkdown
Warning: 1 results truncated (100%) that were invalid MICs: "testvalue"
NOTE: Using column `mo` as input for `col_mo`.
Warning: Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.
--- finished re-building 'SPSS.Rmd'

--- re-building ‘WHONET.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

--- finished re-building ‘WHONET.Rmd’

--- re-building ‘atc_property.Rmd’ using rmarkdown
--- finished re-building 'atc_property.Rmd'

--- re-building ‘benchmarks.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

--- finished re-building ‘benchmarks.Rmd’

--- re-building ‘freq.Rmd’ using rmarkdown
--- finished re-building ‘freq.Rmd’

--- re-building ‘mo_property.Rmd’ using rmarkdown
--- finished re-building 'mo_property.Rmd'

--- re-building ‘resistance_predict.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

Quitting from lines 82-86 (resistance_predict.Rmd) 
Error: processing vignette 'resistance_predict.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘resistance_predict.Rmd’

SUMMARY: processing the following files failed:
  ‘AMR.Rmd’ ‘resistance_predict.Rmd’

Error: Vignette re-building failed.
Execution halted