neurocStats: Package that retrieves Neuroconductor stats

Installing the neurocStats package

You can install neurocStats from github with:

# install.packages("devtools")
> devtools::install_github("adigherman/neurocStats")

Listing all Neuroconductor packages

To get a full list of Neuroconductor packages, the function get_package_list() can be used:

> neuroconductor_packages <- get_package_list()
> head(neuroconductor_packages)
       name                                                                                   title      maintainer     type
1       aal                                               Automated Anatomical Labeling (AAL) Atlas  John Muschelli standard
2     afnir                          Wrapper Functions for AFNI (Analysis of FunctionalNeuroImages)  John Muschelli standard
3     ANTsR                                   ANTs in R: Quantification Tools for Biomedical Images Brian B. Avants standard
4 ANTsRCore                                                  Core Software Infrastructure for ANTsR Brian B. Avants standard
5   bftools                                                                        BioFormats Tools  John Muschelli standard
6 brainKCCA Region-level Connectivity Network Construction via KernelCanonical Correlation Analysis       Jian Kang standard

Retrieve Neuroconductor package description

To get the DESCRIPTION file content for a specific Neuroconductor package we’ll use the get_package_description() function:

> fslr_description <- get_package_description('fslr')
> fslr_details
Type: Package
Package: fslr
Title: Wrapper Functions for FSL ('FMRIB' Software Library) from
    Functional MRI of the Brain ('FMRIB')
Version: 2.17.3
Authors@R (parsed):
    * John Muschelli <muschellij2@gmail.com> [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Description: Wrapper functions that interface with 'FSL'
    <http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/>, a powerful and commonly-used
    'neuroimaging' software, using system commands. The goal is to be able
    to interface with 'FSL' completely in R, where you pass R objects of
    class 'nifti', implemented by package 'oro.nifti', and the function
    executes an 'FSL' command and returns an R object of class 'nifti' if
    desired.
License: GPL-3
BugReports: https://github.com/muschellij2/fslr/issues
Depends:
    oro.nifti (>= 0.5.0),
    neurobase,
    R (>= 3.2.0)
Imports:
    methods,
    matrixStats,
    R.utils,
    graphics,
    grDevices,
    stats,
    utils
Suggests:
    knitr,
    rmarkdown,
    covr
VignetteBuilder: knitr
biocViews:
Encoding: UTF-8
Remotes:
    neuroconductor/oro.nifti@b2b5e408785973e074bdf2f520720a79c23b6ffa,
    neuroconductor/neurobase@a8c7908b98784ee2373508c5d4212659e7b90a9a
RoxygenNote: 6.0.1.9000
SystemRequirements: FSL

Retrieve Neuroconductor package description

To get the full package details for a specific Neuroconductor package

> fslr_details <- get_package_details('fslr')

Get download statistics

The get download statistics we can use the get_download_stats() function. The function accepts the following parameters: package indicating the name of the package for which we need download counts. If package is missing or NULL, the download counts for all Neuroconductor packages are returned. The second argument is verbose which will provide a compact result (when verbose is missing / FALSE) (total number of downloads) versus a detailed list of downloads that will include the package name, version, type of download (for which platform), country from where the download was initiated and the timestamp for the request.

> total_downloads <- get_download_stats()
> head(total_downloads)
    package downloads
1     afnir         7
2     ANTsR        80
3 ANTsRCore        75
4    brainR         3
5     cifti       112
6  dcemriS4         3
> Rxnat_downloads_verbose <- get_download_stats('Rxnat', verbose = TRUE)
> head(Rxnat_downloads_verbose)
   name package_version country os_type r_version   timestamp
1 Rxnat      0.0.0.9005      FR     src             2019-03-22 10:23:38
2 Rxnat      0.0.0.9005      FR     osx       3.5   2019-04-08 01:25:18
3 Rxnat      0.0.0.9005      FI     src             2019-04-26 07:41:12
4 Rxnat      0.0.0.9005      US     win       3.5   2019-04-26 13:36:29
5 Rxnat      0.0.0.9005      DE     osx       3.5   2019-04-26 17:32:54
6 Rxnat      0.0.0.9005      FR     osx       3.5   2019-06-02 00:13:34

List available Neuroconductor releases

To get a list with all available Neuroconductor releases, we’ll use the list_releases() function.

> list_releases()
           release folder
1       releases/2017/nov
2       releases/2018/feb
3 releases/latest/current
4  releases/latest/stable

Get release details

To get a comprehensive list of package details for a specific release we’ll use the get_release_details() function.

> release_details <- get_release_details(year = "2017", month = "nov", os = "osx")
> head(release_details,1)
  Package Version                       Imports Suggests License                           MD5sum Depends LinkingTo Archs Enhances
1   afnir   0.4.4 methods, oro.nifti, neurobase     covr   GPL-2 389bac94bd7e8a677c946c2349ebd070    <NA>      <NA>  <NA>     <NA>