R Observatory: Metrics for atlas version 1.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

atlas

1.0.0Package record

Stanford 'ATLAS' Search Engine API

0packages depend

3.3Kdownloads / year

4.0%test coverage

9/13flavors OK

Overview

About

Maintained by Vladimir PolonyCRAN page ↗Website ↗

Stanford 'ATLAS' (Advanced Temporal Search Engine) is a powerful tool that allows constructing cohorts of patients extremely quickly and efficiently. This package is designed to interface directly with an instance of 'ATLAS' search engine and facilitates API queries and data dumps. Prerequisite is a good knowledge of the temporal language to be able to efficiently construct a query. More information available at https://shahlab.stanford.edu/start.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("atlas", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-atlas

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-atlas

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-atlas

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

4NOTE9OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Vladimir Polony <podalv@gmail.com>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: person(given = "Vladimir",
                    family = "Polony",
                    role = c("aut", "cre"),
                    email = "podalv@gmail.com")
as necessary.

NOTEdependencies in R coder-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘testthat’
All declared Imports should be used.

Additional issues

donttest

CRAN check page ↗

Slowest check: 52 s · r-devel-windows-x86_64

Status changes

NOTE9 OK, 4 NOTENow
NOTE7 OK, 7 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.0

READMENoVignettesNoNEWSNoCitation fileNoWebsiteYes

Help pages: 6
Examples that run: 0%6 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

3.3K

CRAN downloads in the past year

Rank #11,861 · ~9/day · ~277/mo

Releases R versions

Daily download trend is not available in this view yet.

29230 days

92690 days

3.3K1 year

Compare downloads with other packages →

Also on81 r2u10 autocran

How downloads are counted

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing atlas adds 30 packages (16 with compiled code, 8.5 MB of source tarballs). Heaviest: fs 1.4 MB, openssl 1.1 MB, jsonlite 1.0 MB.

Depends (0)

none

Imports (2)

httr testthat

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (from the free-text Author field) (1)

Vladimir Polony

Maintainer since 0.5.0 (2018)

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.0Latest
record
2018-08-10 · current release · diff ↗ ·
added 3 exports
atlas.status, atlas.dump, atlas.contains
0.6.0
record
2018-06-01 · diff ↗
0.5.0
record
2018-05-29
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-05-29
Total releases: 3 / 8 yrs
License: GPL-3 OSI
Download size: 4.1 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("atlas")

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for atlas version 1.0.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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