Error(s) in re-building vignettes:
--- re-building 'continuous.Rmd' using rmarkdown
Loading required package: sp
Loading required package: viridisLite

Attaching package: 'data.table'

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

    shift

Quitting from lines 394-413 (continuous.Rmd) 
Error: processing vignette 'continuous.Rmd' failed with diagnostics:
package or namespace load failed for 'dplyr' in library.dynam(lib, package, package.lib):
 DLL 'dplyr' not found: maybe not installed for this architecture?
--- failed re-building 'continuous.Rmd'

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

Packages 'ggplot2' and 'dplyr' are needed for plotting this figure.
--- finished re-building 'discrete.Rmd'

--- re-building 'none.Rmd' using rmarkdown
Quitting from lines 165-177 (none.Rmd) 
Error: processing vignette 'none.Rmd' failed with diagnostics:
package or namespace load failed for 'dplyr' in library.dynam(lib, package, package.lib):
 DLL 'dplyr' not found: maybe not installed for this architecture?
--- failed re-building 'none.Rmd'

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

--- finished re-building 'nosoi.Rmd'

--- re-building 'output.Rmd' using rmarkdown
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`.
Packages 'ape', 'tidytree' and 'treeio' are needed for transmission tree generation.
Packages 'ggplot2' and 'ggtree' are needed for plotting this figure.
Packages 'ape', 'tidytree' and 'treeio' are needed for transmission tree generation.
Packages 'ape', 'tidytree' and 'treeio' are needed for transmission tree generation.
Package 'ggtree' is needed for plotting this figure.
Packages 'ape', 'tidytree' and 'treeio' are needed for transmission tree generation.
Packages 'ape', 'tidytree' and 'treeio' are needed for transmission tree generation.
Packages 'ape', 'tidytree', 'treeio' and 'ggtree' are needed for transmission tree generation.
--- finished re-building 'output.Rmd'

SUMMARY: processing the following files failed:
  'continuous.Rmd' 'none.Rmd'

Error: Vignette re-building failed.
Execution halted