install allows you to install one of two collections of nat packages

  • core a minimal install that can help users to get started with nat and already solve many problems (the default)

  • natverse a powerful "batteries included" distribution with all mature packages in the natverse.

Since the natverse option will install many packages from GitHub, you need to have a GitHub account and personal access token (GITHUB_PAT). Install will check to see if you have a GITHUB_PAT already and, if not, walk you through the steps of setting one up. A fall-back PAT is built into the package but we strongly recommend that you sign up to GitHub and get your own if you start using the natverse regularly.

check_pat can be used to check if you have a GITHUB_PAT set and will advise on how to do this if necessary.

  collection = c("core", "natverse"),
  pkgs = NULL,
  dependencies = TRUE,
  upgrade.dependencies = "always",

check_pat(create = TRUE)



The collection of natverse packages that you would like to install. The current options are core, the default, or natverse. See Description for more information.


A character vector of package names specifying natverse packages to install. When present overrides the collection argument.


Which dependencies you want to install see install_github.


Whether to install dependencies of natmanager. See the upgrade argument of install_github for details. The default will go ahead and always do this is as necessary.


extra arguments to pass to install_github.


Whether to help you create a personal GITHUB_PAT if you do not have one set. When create=FALSE a default PAT will be used if you have not set your own. This could cause trouble if other people are using the same PAT.


check_pat returns the PAT invisibly or errors out if create=TRUE and none can be set.


if (FALSE) { # install core packages to try out the core natverse natmanager::install('core') # Full "batteries included" installation with all packages natmanager::install('natverse') # Install natverse, non-natverse package # for natverse packages no need to specify the repo natmanager::install(pkgs=c('nat.jrcbrains','flyconnectome/hemibrainr')) } if (FALSE) { # Check status of GitHub PAT and create one if required natmanager::check_pat(create=TRUE) # Check status of GitHub PAT and use default if no personal one available natmanager::check_pat(create=FALSE) }