Error(s) in re-building vignettes:
  ...
--- re-building ‘continuous.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
Loading required package: viridisLite

Attaching package: 'data.table'

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

    shift


Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

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

    intersect, select, union

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 ‘continuous.Rmd’

--- re-building ‘discrete.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: viridisLite

Attaching package: 'igraph'

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

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

    union

Quitting from lines 44-65 (discrete.Rmd) 
Error: processing vignette 'discrete.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘discrete.Rmd’

--- re-building ‘none.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘none.Rmd’

--- re-building ‘nosoi.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: viridisLite

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Quitting from lines 42-68 (nosoi.Rmd) 
Error: processing vignette 'nosoi.Rmd' failed with diagnostics:
$ operator is invalid for atomic vectors
--- failed re-building ‘nosoi.Rmd’

--- re-building ‘output.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: data.table
Starting the simulation
Initializing ... running ...
Time: 10 (10% of maximum length). Hosts count: 13 (6% of maximum infected hosts).
Time: 20 (20% of maximum length). Hosts count: 88 (44% of maximum infected hosts).
Time: 30 (30% of maximum length). Hosts count: 120 (60% of maximum infected hosts).
Time: 40 (40% of maximum length). Hosts count: 171 (86% of maximum infected hosts).
done. 
The simulation has run for 46 units of time and a total of 204 hosts have been infected.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
ggtree v2.0.1  For help: https://yulab-smu.github.io/treedata-book/

If you use ggtree in published research, please cite the most appropriate paper(s):

[36m-[39m Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi: 10.1093/molbev/msy194
[36m-[39m Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628



Attaching package: 'dplyr'

The following objects are masked from 'package:data.table':

    between, first, last

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 ‘output.Rmd’

SUMMARY: processing the following files failed:
  ‘discrete.Rmd’ ‘nosoi.Rmd’

Error: Vignette re-building failed.
Execution halted