Package: osutils 0.0.0.9000

William Hulme

osutils: Useful Functions for OpenSAFELY

Contains functions that are often needed when using the OpenSAFELY platform <https://www.opensafely.org/>, such as redaction and low-memory processing.

Authors:William Hulme [aut, cre], Tom Palmer [aut]

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osutils.pdf |osutils.html✨
osutils/json (API)

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

Peer review:

Bug tracker:https://github.com/wjchulme/osutils/issues

On CRAN:

1.70 score 1 scripts 30 exports 77 dependencies

Last updated 2 years agofrom:ed6804e952. Checks:OK: 5 NOTE: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 14 2024
R-4.5-winNOTEOct 14 2024
R-4.5-linuxNOTEOct 14 2024
R-4.4-winOKOct 14 2024
R-4.4-macOKOct 14 2024
R-4.3-winOKOct 14 2024
R-4.3-macOKOct 14 2024

Exports:%>%action_names_to_txtc_actiongt_catgt_catcatgt_catnumgt_numpipeline_actionpipeline_commentpipeline_listproject_list_to_yamlreadtype_csvreadtype_delimredact_tblsummaryredacted_summary_catredacted_summary_catcatredacted_summary_catnumredacted_summary_dateredacted_summary_numredactorredactor2reformat_codelistsround_kmsample_nonoutcomes_nsample_nonoutcomes_propsample_random_nsample_random_propsample_weightswritetype_csvwritetype_delim

Dependencies:backportsbase64encbigDbitbit64bitopsbroombslibcachemclicliprcolorspacecommonmarkcpp11crayoncurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomeforcatsfsgenericsgluegthighrhmshtmltoolshtmlwidgetsjquerylibjsonlitejuicyjuiceknitrlabelinglifecyclemagrittrmarkdownmemoisemimemunsellpillarpkgconfigplyrprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreactablereactRreadrrlangrmarkdownsassscalesstringistringrtibbletidyrtidyselecttinytextzdbutf8V8vctrsviridisLitevroomwithrxfunxml2yaml

Readme and manuals

Help Manual

Help pageTopics
Put action names in a txt file --action_names_to_txt
Create comment objectc_action
Convert output of categorical tabulation (redacted_summary_cat) to gt objectgt_cat
Convert output of categorical cross-tabulation (redacted_summary_catcat) to gt objectgt_catcat
Convert output of categorical-numeric cross-tabulation (redacted_summary_catnum) to gt objectgt_catnum
Convert output of numeric tabulation (redact_summary_num) to gt objectgt_num
Create action objectpipeline_action
Create comment objectpipeline_comment
Create entire pipeline listpipeline_list
Convert list to yaml and saveproject_list_to_yaml
Read a csv file into a tibble, and type columns using a separate json file.readtype_csv
Read a delimited file (including CSV and TSV) into a tibble, and type columns using a separate json filereadtype_delim
Redact tbl_summary objectredact_tblsummary
Summarise a categorical variable and redact if necessaryredacted_summary_cat
Categorical by categorical cross-tabulation, with redaction if necessaryredacted_summary_catcat
Categorical by numeric cross-tabulation, with redaction if necessaryredacted_summary_catnum
Redact a date vectorredacted_summary_date
Summarise a numeric vector and redact if necessaryredacted_summary_num
Indicates which values to redact from a vector of frequenciesredactor
Redact values in a vector based on frequency valuesredactor2
Converts a json file of codelist names and URLs into an HTML tablereformat_codelists
Rounded Kaplan-Meier curvesround_km
Sample patients (or other observational units) based on patient IDs, depending on occurrence of an event or notsample_nonoutcomes_n
Sample patients (or other observational units) based on patient IDs, depending on occurrence of an event or notsample_nonoutcomes_prop
Sample n patients (or other observational units) based on patient IDs.sample_random_n
Sample a proportion of patients (or other observational units) based on patient IDssample_random_prop
Derive sampling probabilitiessample_weights
Write a data frame to a csv file, and save typing information in a separate json filewritetype_csv
Write a data frame to a delimited file, and save typing information in a separate json filewritetype_delim