R: Reproducible Pipeline Infrastructure for Neuroscience

# Reproducible Pipeline Infrastructure for Neuroscience

## Documentation for package ‘ravepipeline’ version 0.0.3

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

A B C D G I L M P R S U W

## -- A --

add_module_registry | 'RAVE' module registry

## -- B --

base64-utils | Convert from and to 'base64' string
base64_decode | Convert from and to 'base64' string
base64_encode | Convert from and to 'base64' string
base64_plot | Convert from and to 'base64' string
base64_urldecode | Convert from and to 'base64' string
base64_urlencode | Convert from and to 'base64' string

## -- C --

check_job | Run a function (job) in another session
configure_knitr | Configure "rmarkdown" files to build 'RAVE' pipelines

## -- D --

dir_create2 | Force creating directory with checks

## -- G --

get_modules_registries | 'RAVE' module registry
get_module_description | 'RAVE' module registry

## -- I --

install_modules | Install 'RAVE' modules
install_snippet | 'RAVE' code snippets

## -- L --

lapply_jobs | Internal parallel functions
list_snippets | 'RAVE' code snippets
load_snippet | 'RAVE' code snippets
load_targets | Low-level 'RAVE' pipeline functions
load_yaml | Read write "YAML" format
logger | Logger system used by 'RAVE'
logger_error_condition | Logger system used by 'RAVE'
logger_threshold | Logger system used by 'RAVE'

## -- M --

module_add | Add new 'RAVE' (2.0) module to current project
module_registry | 'RAVE' module registry
module_registry2 | 'RAVE' module registry

## -- P --

pipeline | Creates 'RAVE' pipeline instance
pipeline-knitr-markdown | Configure "rmarkdown" files to build 'RAVE' pipelines
PipelineCollections | Connect and schedule pipelines
PipelineResult | Class definition for 'RAVE' pipeline results
PipelineTools | Class definition for 'RAVE' pipelines
pipeline_attach | Low-level 'RAVE' pipeline functions
pipeline_build | Low-level 'RAVE' pipeline functions
pipeline_clean | Low-level 'RAVE' pipeline functions
pipeline_collection | Combine and execute pipelines
pipeline_create_subject_pipeline | Low-level 'RAVE' pipeline functions
pipeline_create_template | Low-level 'RAVE' pipeline functions
pipeline_debug | Low-level 'RAVE' pipeline functions
pipeline_dep_targets | Low-level 'RAVE' pipeline functions
pipeline_description | Low-level 'RAVE' pipeline functions
pipeline_eval | Low-level 'RAVE' pipeline functions
pipeline_find | Low-level 'RAVE' pipeline functions
pipeline_fork | Low-level 'RAVE' pipeline functions
PIPELINE_FORK_PATTERN | Constant variables used in 'RAVE' pipeline
pipeline_from_path | Creates 'RAVE' pipeline instance
pipeline_get_preferences | Low-level 'RAVE' pipeline functions
pipeline_hasname | Low-level 'RAVE' pipeline functions
pipeline_has_preferences | Low-level 'RAVE' pipeline functions
pipeline_install | Install 'RAVE' pipelines
pipeline_install_github | Install 'RAVE' pipelines
pipeline_install_local | Install 'RAVE' pipelines
pipeline_list | Low-level 'RAVE' pipeline functions
pipeline_load_extdata | Low-level 'RAVE' pipeline functions
pipeline_progress | Low-level 'RAVE' pipeline functions
pipeline_read | Low-level 'RAVE' pipeline functions
pipeline_render | Configure "rmarkdown" files to build 'RAVE' pipelines
pipeline_root | Low-level 'RAVE' pipeline functions
pipeline_run | Low-level 'RAVE' pipeline functions
pipeline_run_bare | Low-level 'RAVE' pipeline functions
pipeline_save_extdata | Low-level 'RAVE' pipeline functions
pipeline_settings_get | Get or change pipeline input parameter settings
pipeline_settings_get_set | Get or change pipeline input parameter settings
pipeline_settings_set | Get or change pipeline input parameter settings
pipeline_setup_rmd | Configure "rmarkdown" files to build 'RAVE' pipelines
pipeline_set_preferences | Low-level 'RAVE' pipeline functions
pipeline_shared | Low-level 'RAVE' pipeline functions
pipeline_target_names | Low-level 'RAVE' pipeline functions
pipeline_vartable | Low-level 'RAVE' pipeline functions
pipeline_visualize | Low-level 'RAVE' pipeline functions
pipeline_watch | Low-level 'RAVE' pipeline functions

## -- R --

rave-pipeline | Low-level 'RAVE' pipeline functions
rave-pipeline-jobs | Run a function (job) in another session
rave-serialize-refhook | Serialization reference hook generic functions
rave-snippet | 'RAVE' code snippets
RAVEFileArray | 'R6' wrapper for "FileArray"
raveio-option | Set/Get 'RAVE' option
raveio_confpath | Set/Get 'RAVE' option
raveio_getopt | Set/Get 'RAVE' option
raveio_resetopt | Set/Get 'RAVE' option
raveio_setopt | Set/Get 'RAVE' option
ravepipeline-constants | Constant variables used in 'RAVE' pipeline
ravepipeline_finalize_installation | Download 'RAVE' built-in pipelines and code snippets
RAVESerializable | Abstract class for 'RAVE' serialization
rave_progress | 'RAVE' progress
rave_serialize_impl | Serialization reference hook generic functions
rave_serialize_impl.default | Serialization reference hook generic functions
rave_serialize_impl.rave-brain | Serialization reference hook generic functions
rave_serialize_impl.RAVESerializable | Serialization reference hook generic functions
rave_serialize_refhook | Serialization reference hook generic functions
rave_unserialize_impl | Serialization reference hook generic functions
rave_unserialize_impl.default | Serialization reference hook generic functions
rave_unserialize_impl.rave_serialized | Serialization reference hook generic functions
rave_unserialize_impl.rave_serialized_r6 | Serialization reference hook generic functions
rave_unserialize_impl.rave_serialized_rave-brain | Serialization reference hook generic functions
rave_unserialize_refhook | Serialization reference hook generic functions
read-write-yaml | Read write "YAML" format
remove_job | Run a function (job) in another session
resolve_job | Run a function (job) in another session

## -- S --

save_yaml | Read write "YAML" format
set_logger_path | Logger system used by 'RAVE'
start_job | Run a function (job) in another session

## -- U --

update_local_snippet | 'RAVE' code snippets

## -- W --

with_rave_parallel | Internal parallel functions