Package: ravepipeline 0.1.0

ravepipeline: Reproducible Pipeline Infrastructure for Neuroscience

Defines the underlying pipeline structure for reproducible neuroscience, adopted by 'RAVE' (reproducible analysis and visualization of intracranial electroencephalography); provides high-level class definition to build, compile, set, execute, and share analysis pipelines. Both R and 'Python' are supported, with 'Markdown' and 'shiny' dashboard templates for extending and building customized pipelines. See the full documentations at <https://rave.wiki>; to cite us, check out our paper by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>), or run citation("ravepipeline") for details.

Authors:Zhengjia Wang [aut, cre, cph], John Magnotti [ctb, res], Xiang Zhang [ctb, res], Michael Beauchamp [ctb, res], Trustees of University of Pennsylvania [cph]

ravepipeline_0.1.0.tar.gz
ravepipeline_0.1.0.zip(r-4.7)ravepipeline_0.1.0.zip(r-4.6)ravepipeline_0.1.0.zip(r-4.5)
ravepipeline_0.1.0.tgz(r-4.6-any)ravepipeline_0.1.0.tgz(r-4.5-any)
ravepipeline_0.1.0.tar.gz(r-4.7-any)ravepipeline_0.1.0.tar.gz(r-4.6-any)
ravepipeline_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ravepipeline/json (API)
NEWS

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

Bug tracker:https://github.com/dipterix/ravepipeline/issues

Pkgdown/docs site:https://dipterix.org

On CRAN:

Conda:

5.40 score 2 packages 42 scripts 561 downloads 97 exports 49 dependencies

Last updated from:c397a51507. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK191
source / vignettesOK218
linux-release-x86_64OK187
macos-release-arm64OK108
macos-oldrel-arm64OK199
windows-develOK145
windows-releaseOK134
windows-oldrelOK130
wasm-releaseOK150

Exports:%...!%%...>%%...T!%%...T>%add_module_registryas.promisebase64_decodebase64_encodebase64_plotbase64_urldecodebase64_urlencodecheck_jobconfigure_knitrdigestdir_create2get_module_descriptionget_modules_registriesgluehtml_embed_readhtml_embed_writeinstall_modulesinstall_snippetlapply_jobslist_snippetsload_snippetload_targetsload_yamlloggerlogger_error_conditionlogger_thresholdmodule_addmodule_registrymodule_registry2pipelinepipeline_attachpipeline_buildpipeline_cleanpipeline_collectionpipeline_create_subject_pipelinepipeline_create_templatepipeline_debugpipeline_dep_targetspipeline_descriptionpipeline_evalpipeline_export_wizardpipeline_findpipeline_forkPIPELINE_FORK_PATTERNpipeline_from_pathpipeline_get_preferencespipeline_has_preferencespipeline_hasnamepipeline_import_wizardpipeline_install_githubpipeline_install_localpipeline_listpipeline_load_extdatapipeline_plot_datapipeline_progresspipeline_readpipeline_renderpipeline_rootpipeline_runpipeline_run_barepipeline_save_extdatapipeline_set_preferencespipeline_settings_getpipeline_settings_setpipeline_setup_rmdpipeline_sharedpipeline_target_namespipeline_translate_settingspipeline_vartablepipeline_visualizepipeline_watchPipelineCollectionsPipelineResultPipelineToolsrave_progressrave_serialize_implrave_serialize_refhookrave_unserialize_implrave_unserialize_refhookRAVEFileArrayraveio_confpathraveio_getoptraveio_resetoptraveio_setoptravepipeline_finalize_installationRAVESerializableremove_jobresolve_jobsave_yamlset_logger_pathstart_jobupdate_local_snippetwith_rave_parallel

Dependencies:backportsbase64encbase64urlcallrclicodetoolscpp11data.tabledigestevaluatefastmapfstfstcorefutureglobalsgluehighrigraphjsonliteknitrlaterlatticelifecyclelistenvloggermagrittrMatrixotelparallellypillarpkgconfigprettyunitsprocessxpromisespsR6Rcppremotesrlangsecretbasetargetstibbletidyselectutf8uuidvctrswithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Convert from and to 'base64' stringbase64-utils base64_decode base64_encode base64_plot base64_urldecode base64_urlencode
Force creating directory with checksdir_create2
Embed binary data or JSON strings into HTML fileshtml-embed html_embed_read html_embed_write
Install 'RAVE' modulesinstall_modules
Logger system used by 'RAVE'logger logger_error_condition logger_threshold set_logger_path
Add new 'RAVE' (2.0) module to current projectmodule_add
'RAVE' module registryadd_module_registry get_modules_registries get_module_description module_registry module_registry2
Creates 'RAVE' pipeline instancepipeline pipeline_from_path
Combine and execute pipelinespipeline_collection
Install 'RAVE' pipelinespipeline_install pipeline_install_github pipeline_install_local
Create plot data from within pipeline make-filepipeline_plot_data
Get or change pipeline input parameter settingspipeline_settings_get pipeline_settings_get_set pipeline_settings_set
Translate pipeline settings between pipelinespipeline_export_wizard pipeline_import_wizard pipeline_translate_settings
Configure ''rmarkdown'' files to build 'RAVE' pipelinesconfigure_knitr pipeline-knitr-markdown pipeline_render pipeline_setup_rmd
Connect and schedule pipelinesPipelineCollections
Class definition for 'RAVE' pipeline resultsPipelineResult
Class definition for 'RAVE' pipelinesPipelineTools
'RAVE' progressrave_progress
Low-level 'RAVE' pipeline functionsload_targets pipeline_attach pipeline_build pipeline_clean pipeline_create_subject_pipeline pipeline_create_template pipeline_debug pipeline_dep_targets pipeline_description pipeline_eval pipeline_find pipeline_fork pipeline_hasname pipeline_list pipeline_load_extdata pipeline_progress pipeline_read pipeline_root pipeline_run pipeline_run_bare pipeline_save_extdata pipeline_shared pipeline_target_names pipeline_vartable pipeline_visualize pipeline_watch rave-pipeline
Run a function (job) in another sessioncheck_job rave-pipeline-jobs remove_job resolve_job start_job
Pipeline preference management (low-level)pipeline_get_preferences pipeline_has_preferences pipeline_set_preferences rave-pipeline-preferences
Serialization reference hook generic functionsrave-serialize-refhook rave_serialize_impl rave_serialize_impl.default rave_serialize_impl.rave-brain rave_serialize_impl.RAVESerializable rave_serialize_refhook rave_unserialize_impl rave_unserialize_impl.default rave_unserialize_impl.rave_serialized rave_unserialize_impl.rave_serialized_r6 rave_unserialize_impl.rave_serialized_rave-brain rave_unserialize_refhook
'RAVE' code snippetsinstall_snippet list_snippets load_snippet rave-snippet update_local_snippet
'R6' wrapper for ''FileArray''RAVEFileArray
Set/Get 'RAVE' optionraveio-option raveio_confpath raveio_getopt raveio_resetopt raveio_setopt
Download 'RAVE' built-in pipelines and code snippetsravepipeline_finalize_installation
Constant variables used in 'RAVE' pipelinePIPELINE_FORK_PATTERN ravepipeline-constants
Abstract class for 'RAVE' serializationRAVESerializable
Read write ''YAML'' formatload_yaml read-write-yaml save_yaml
Internal parallel functionslapply_jobs with_rave_parallel