The natverse package is a wrapper for all of the commonly used
NeuroAnatomy Toolbox packages. This is convenient both for package
installation and for loading/attaching these packages without many calls
to library().
See http://natverse.org for more details.
The recommended approach to install the full natverse is to use a helper package natmanager, which is available on CRAN. You can therefore do:
install.packages("natmanager")
natmanager::install("natverse")See http://natverse.org/install for more details.
Once installed, you can load the natverse package:
library(natverse)
#> Loading required package: elmr
#> Loading required package: catmaid
#> Loading required package: httr
#> Warning: package 'httr' was built under R version 3.6.2
#> Loading required package: nat
#> Loading required package: rgl
#> Warning: package 'rgl' was built under R version 3.6.2
#> Registered S3 method overwritten by 'nat':
#> method from
#> as.mesh3d.ashape3d rgl
#>
#> Attaching package: 'nat'
#> The following object is masked from 'package:rgl':
#>
#> wire3d
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, union
#> Loading required package: nat.flybrains
#> Loading required package: nat.templatebrains
#> Loading required package: nat.nblast
# example 3D plot of some neurons
plot(kcs20, col=type)
The natverse package contains many packages and it is possible that there could be conflicts where functions in the natverse have the same name as another package.
natverse_conflicts()
#> ── Conflicts ─────────────────────────────────────────────────────────────── natverse_conflicts() ──
#> x nat::intersect() masks base::intersect()
#> x nat::setdiff() masks base::setdiff()
#> x nat::union() masks base::union()
#> x nat::wire3d() masks rgl::wire3d()You can always choose the correct version by prepending the specific
package name e.g. nat::flip() will select the nat version rather than
any other.
Once installed, you check the status of all natverse packages and their dependencies like so:
natverse_update()
#>
#> The following packages are either locally installed or information about them is missing!
#>
#> blob, formattable, import, mockr, nycflights13, pingr, fafbsegdata, reticulate, nat
#>
#> Please install them manually from their appropriate source locations
#>
#> The following natverse dependencies are out-of-date, see details below:
#>
#> We recommend updating them by running:
#> natverse_update(update=TRUE)
#>
#> package remote local source repo status
#> -------------- ------------- ------------- ------- -------------------------- -------
#> bit64 0.9-7.1 0.9-7 CRAN https://cran.rstudio.com/ x
#> data.table 1.13.0 1.12.8 CRAN https://cran.rstudio.com/ x
#> elmr deb0e27df... 7a2be4537... GitHub natverse x
#> ff 2.2-14.2 2.2-14 CRAN https://cran.rstudio.com/ x
#> flycircuit 1b7b48e29... cc4594f47... GitHub natverse x
#> git2r 0.27.1 0.26.1 CRAN https://cran.rstudio.com/ x
#> insectbrainr 6331b4df6... 8fef94a05... GitHub natverse x
#> mouselightr 9c2ce1c31... 8e26b7702... GitHub natverse x
#> nat.flybrains 28ff33213... 36c622a15... GitHub natverse x
#> nat.jrcbrains 85ed4a791... 44c95667e... GitHub natverse x
#> neuprintr 7403d3ce2... 8ab03b744... GitHub natverse x
#> RCurl 1.98-1.2 1.98-1.1 CRAN https://cran.rstudio.com/ x
#> tibble b4eec19dd... 3f4e5dfae... GitHub tidyverse x
#> tidyr 1.1.0 1.0.3 CRAN https://cran.rstudio.com/ x
#> xfun 0.16 0.15 CRAN https://cran.rstudio.com/ x
#> XML NA 3.99-0.3 CRAN https://cran.rstudio.com/ xYou can then update like so:
natverse_update(update = TRUE)However, if you are in a hurry and want to save time from the questions use like below:
natverse_update(update=TRUE, upgrade = 'always')If want to upgrade the natverse package itself:
remotes::update_packages('natverse')