Package: hubUtils 0.5.0

Anna Krystalli

hubUtils: Core 'hubverse' Utilities

Core set of low-level utilities common across the 'hubverse'. Used to interact with 'hubverse' schema, Hub configuration files and model outputs and designed to be primarily used internally by other 'hubverse' packages. See Reich et al. (2022) <doi:10.2105/AJPH.2022.306831> for an overview of Collaborative Hubs.

Authors:Anna Krystalli [aut, cre], Li Shandross [ctb], Nicholas G. Reich [ctb], Evan L. Ray [ctb], Zhian N. Kamvar [ctb], Consortium of Infectious Disease Modeling Hubs [cph]

hubUtils_0.5.0.tar.gz
hubUtils_0.5.0.zip(r-4.5)hubUtils_0.5.0.zip(r-4.4)hubUtils_0.5.0.zip(r-4.3)
hubUtils_0.5.0.tgz(r-4.5-any)hubUtils_0.5.0.tgz(r-4.4-any)hubUtils_0.5.0.tgz(r-4.3-any)
hubUtils_0.5.0.tar.gz(r-4.5-noble)hubUtils_0.5.0.tar.gz(r-4.4-noble)
hubUtils_0.5.0.tgz(r-4.4-emscripten)hubUtils_0.5.0.tgz(r-4.3-emscripten)
hubUtils.pdf |hubUtils.html✨
hubUtils/json (API)
NEWS

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

Bug tracker:https://github.com/hubverse-org/hubutils/issues

Pkgdown site:https://hubverse-org.github.io

Datasets:

On CRAN:

Conda:

hubverse

7.22 score 6 stars 7 packages 49 scripts 547 downloads 44 exports 32 dependencies

Last updated 10 days agofrom:93617b509c (on v0.5.0). Checks:6 OK, 3 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 12 2025
R-4.5-winNOTEMar 12 2025
R-4.5-macNOTEMar 12 2025
R-4.5-linuxNOTEMar 12 2025
R-4.4-winOKMar 12 2025
R-4.4-macOKMar 12 2025
R-4.4-linuxOKMar 12 2025
R-4.3-winOKMar 12 2025
R-4.3-macOKMar 12 2025

Exports:%>%as_configas_model_out_tblcheck_deprecated_schemacreate_s3_urlextract_schema_versionget_config_tidget_hub_derived_task_idsget_hub_file_formatsget_hub_model_output_dirget_hub_timezoneget_round_idsget_round_idxget_round_model_tasksget_round_task_id_namesget_schemaget_schema_urlget_schema_valid_versionsget_schema_version_latestget_task_id_namesget_version_configget_version_fileget_version_hubis_github_repo_urlis_github_urlis_s3_base_fsis_urlis_v3_configis_v3_config_fileis_v3_hubis_valid_urlmodel_id_mergemodel_id_splitread_configread_config_filesubset_std_colssubset_task_id_colssubset_task_id_namesvalidate_model_out_tblversion_equalversion_gtversion_gteversion_ltversion_lte

Dependencies:askpassbackportscachemcheckmateclicurlfansifastmapfsghgitcredsgluehttr2inijsonlitelifecyclemagrittrmemoiseopensslpillarpkgconfigpurrrR6rappdirsrlangstringistringrsystibbleutf8vctrswithr

Readme and manuals

Help Manual

Help pageTopics
Coerce a config list to a config class objectas_config
Convert model output to a 'model_out_tbl' class object.as_model_out_tbl
Check whether a config file is using a deprecated schemacheck_deprecated_schema
Create a URL to a file in an S3 bucketcreate_s3_url
Extract the schema version from a schema 'id' or config 'schema_version' property character stringextract_schema_version
Get the name of the output type id column based on the schema versionget_config_tid
Get hub configuration fieldsget_hub_derived_task_ids get_hub_file_formats get_hub_model_output_dir get_hub_timezone
Utilities for accessing round ID metadataget_round_ids get_round_idx
Get the model tasks for a given roundget_round_model_tasks
Get task ID names for a given roundget_round_task_id_names
Download a schemaget_schema
Get the JSON schema download URL for a given config file versionget_schema_url
Get a vector of valid schema versionget_schema_valid_versions
Get the latest schema versionget_schema_version_latest
Get hub task IDsget_task_id_names
Get hub config schema versionsget_version_config get_version_file get_version_hub
Example Hub model output datahub_con_output
Detect if a URL is a GitHub repository URLis_github_repo_url
Detect a URL on github.comis_github_url
Detect whether An object of class <SubTreeFileSystem> represents the base path of an S3 file system (i.e. the root of a cloud hub)is_s3_base_fs
Determine if a string is a URLis_url
Is config list representation using v3.0.0 schema?is_v3_config
Is config file using v3.0.0 schema?is_v3_config_file
Is hub configured using v3.0.0 schema?is_v3_hub
Determine if a URL is valid and reachableis_valid_url
Merge/Split model output tbl 'model_id' columnmodel_id_merge model_id_split
Read a hub config file into Rread_config
Read a JSON config file from a pathread_config_file
Hubverse model output standard column namesstd_colnames
Subset a 'model_out_tbl' or submission 'tbl'.subset_std_cols subset_task_id_cols
Subset a vector of column names to only include task IDssubset_task_id_names
Validate a 'model_out_tbl' object.validate_model_out_tbl
Compare hub config 'schema_version's to specific version numbers from a variety of sourcesversion_equal version_gt version_gte version_lt version_lte