Package: orderly1 1.7.2

Rich FitzJohn

orderly1: Lightweight Reproducible Reporting

Order, create and store reports from R. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.

Authors:Rich FitzJohn [aut, cre], Robert Ashton [aut], Alex Hill [aut], Martin Eden [aut], Wes Hinsley [aut], Emma Russell [aut], James Thompson [aut], Imperial College of Science, Technology and Medicine [cph]

orderly1_1.7.2.tar.gz
orderly1_1.7.2.zip(r-4.7)orderly1_1.7.2.zip(r-4.6)orderly1_1.7.2.zip(r-4.5)
orderly1_1.7.2.tgz(r-4.6-any)orderly1_1.7.2.tgz(r-4.5-any)
orderly1_1.7.2.tar.gz(r-4.7-any)orderly1_1.7.2.tar.gz(r-4.6-any)
orderly1_1.7.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
orderly1/json (API)

# Install 'orderly1' in R:
install.packages('orderly1', repos = c('https://mrc-ide.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/vimc/orderly/issues

On CRAN:

Conda:

7.83 score 116 stars 2 packages 1 scripts 51 exports 33 dependencies

Last updated from:da33851ab2 (on main). Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK203
source / vignettesOK236
linux-release-x86_64OK228
macos-release-arm64OK137
macos-oldrel-arm64OK126
windows-develOK131
windows-releaseOK117
windows-oldrelOK172
wasm-releaseOK107

Exports:orderly_batchorderly_bundle_importorderly_bundle_import_remoteorderly_bundle_listorderly_bundle_packorderly_bundle_pack_remoteorderly_bundle_runorderly_cancel_remoteorderly_cleanuporderly_commitorderly_configorderly_dborderly_deduplicateorderly_default_remote_getorderly_default_remote_setorderly_develop_cleanorderly_develop_startorderly_develop_statusorderly_exampleorderly_graphorderly_graph_out_of_dateorderly_infoorderly_initorderly_latestorderly_listorderly_list_archiveorderly_list_draftsorderly_list_metadataorderly_logorderly_log_offorderly_log_onorderly_migrateorderly_neworderly_packagesorderly_pull_archiveorderly_pull_dependenciesorderly_push_archiveorderly_rebuildorderly_remoteorderly_remote_pathorderly_remote_statusorderly_runorderly_run_infoorderly_run_remoteorderly_searchorderly_test_checkorderly_test_startorderly_use_gitignoreorderly_use_packageorderly_use_resourceorderly_use_source

Dependencies:askpassbitbit64blobcachemclicpp11crayoncredentialscurlDBIdigestdocoptfastmapfsgertglueidsjsonlitelifecyclememoiseopensslpkgconfigR6rlangRSQLiterstudioapisysuuidvctrswithryamlzip

orderly
Introduction | The problem | The process | Example | Running the report | Creating a report | Resources, sources and artefacts | Using artefacts from other reports | Parameterised reports | Using global resources | Using version control | Using SQL databases | Configuration | Use within a report | Advanced use | Customising the database configuration | Advanced database configuration | Using environment variables and secrets | Developing a report
Rendered fromorderly.Rmdusingknitr::rmarkdown

Last update: 2025-07-11
Started: 2017-06-12

orderly bundles
Overview | The process | Limitations
Rendered frombundles.Rmdusingknitr::rmarkdown

Last update: 2025-07-11
Started: 2020-06-10

orderly changelog
The orderly changelog | User's perspective | Details
Rendered fromchangelog.Rmdusingknitr::rmarkdown

Last update: 2025-07-11
Started: 2018-11-08

orderly patterns
Individual researcher | Why not commit the archive to git? | Small group, sharing via shared disk | Some comments on collaboration | Group of researchers, sharing via server | Using staging environments | Dependency resolution | Looking forward, a fully decentralised approach
Rendered frompatterns.Rmdusingknitr::rmarkdown

Last update: 2025-07-11
Started: 2020-06-03

orderly remotes
OrderlyWeb | Configuring orderly to talk to OrderlyWeb | Interacting with the remote server | Future developments | Deploying a remote server
Rendered fromremote.Rmdusingknitr::rmarkdown

Last update: 2025-07-11
Started: 2019-10-11

Readme and manuals

Help Manual

Help pageTopics
Run a batch of reports.orderly_batch
Pack and run orderly "bundles"orderly_bundle_import orderly_bundle_list orderly_bundle_pack orderly_bundle_run
Pack and import bundles with remotesorderly_bundle_import_remote orderly_bundle_pack_remote
Cancel a reportorderly_cancel_remote
Orderly cleanuporderly_cleanup
Commit a generated reportorderly_commit
Retrieve orderly config object.orderly_config orderly_config_
Connect to orderly databasesorderly_db
Deduplicate an orderly archiveorderly_deduplicate
Set default remote locationorderly_default_remote_get orderly_default_remote_set
Develop an orderly reportorderly_develop_clean orderly_develop_start orderly_develop_status
Set up an orderly exampleorderly_example
Print the dependency tree for a given report using orderly logorderly_graph
Given a tree return a list of reports to be re-run (and the order that they should be re-run)orderly_graph_out_of_date
Return info about a report which has been runorderly_info
Initialise an orderly storeorderly_init
Find most recent reportorderly_latest
List orderly reportsorderly_list
List draft and archived reportsorderly_list_archive orderly_list_drafts
List reports with only local metadataorderly_list_metadata
Orderly logging and diagnostic messagesorderly_log orderly_log_off orderly_log_on
Migrate an orderly archiveorderly_migrate
Create new reportorderly_new
Return details of packages required by all src reports in this orderly repoorderly_packages
Download dependent reportsorderly_pull_archive orderly_pull_dependencies orderly_push_archive
Rebuild the report databaseorderly_rebuild
Get a remoteorderly_remote
Orderly remote at a different pathorderly_remote_path
Get status of remote queue.orderly_remote_status
Run a reportorderly_run
Information on current orderly runorderly_run_info
Run a report on a remote serverorderly_run_remote
Search for orderly reports matching criteriaorderly_search
Prepare a directory for orderly to useorderly_test_check orderly_test_start
Add a resource to orderly.ymlorderly_use_gitignore orderly_use_package orderly_use_resource orderly_use_source