Package: zhncommandR 0.1.0

Raban Heller

zhncommandR: Audit and Analysis Dashboard for Haematological Oncology Cohorts

Reads tumour-documentation spreadsheets from haematological tumour centres and computes quality and coverage indicators, OPS-8-544 complex chemotherapy block counts, OPS-1-941 complex diagnostics counts, Kaplan-Meier analyses, oncoprint and cytogenetics summaries, plus an interactive Shiny dashboard for auditor live evaluation. Includes a fully synthetic example cohort for demonstration and testing.

Authors:Hanno Witte [aut], Raban Heller [aut, cre]

zhncommandR_0.1.0.tar.gz
zhncommandR_0.1.0.zip(r-4.7-any)zhncommandR_0.1.0.zip(r-4.6-any)zhncommandR_0.1.0.zip(r-4.5-any)
zhncommandR_0.1.0.tgz(r-4.6-any)zhncommandR_0.1.0.tgz(r-4.5-any)
zhncommandR_0.1.0.tar.gz(r-4.7-any)zhncommandR_0.1.0.tar.gz(r-4.6-any)
zhncommandR_0.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
zhncommandR/json (API)

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

Bug tracker:https://github.com/cttir/zhncommandr/issues

Pkgdown/docs site:https://cttir.github.io

On CRAN:

Conda:

4.08 score 24 exports 85 dependencies

Last updated from:b43dfcba5b. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK185
source / vignettesOK275
linux-releaseOK157
macos-releaseOK163
macos-oldrelOK125
windows-develOK135
windows-releaseOK132
windows-oldrelOK145
wasm-releaseOK124

Exports:new_cohort_dfnew_diagnostic_blocksnew_therapy_blockszhn_alteration_typezhn_example_pathzhn_is_mutationzhn_km_pairwisezhn_normalize_alterationzhn_palzhn_parse_cytogeneticszhn_parse_oncoprintzhn_plot_cases_by_yearzhn_plot_diagnoseszhn_plot_kmzhn_prepare_diagnostic_blockszhn_prepare_therapy_blockszhn_read_cohortzhn_read_diagnosticszhn_read_therapyzhn_read_tumorboardzhn_register_fontszhn_run_appzhn_save_plotzhn_theme

Dependencies:backportsbase64encbroombsiconsbslibcachemcellrangerclicommonmarkcpp11crayoncrosstalkdigestdplyrDTevaluatefarverfastmapfontawesomefsgenericsggplot2ggsurvfitgluegtablehighrhmshtmltoolshtmlwidgetshttpuvisobandjanitorjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMatrixmemoisemimeotelpatchworkpillarpkgconfigprettyunitsprogresspromisespurrrR6raggrappdirsRColorBrewerRcppreadxlrematchrlangrmarkdownS7sassscalesshinysnakecasesourcetoolsstringistringrsurvivalsystemfontstextshapingtibbletidyrtidyselecttimechangetinytexutf8vctrsviridisLitewithrxfunxtableyaml

Figures and tables
The tables behind the panels | OPS-8-544 therapy blocks | OPS-1-941 complex diagnostics | Oncoprint and cytogenetics | The figures | Exporting paper-ready files
Rendered fromfigures-and-tables.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-06-16

Getting started with zhncommandR
Example data | Reading the cohort | Quality indicators | OPS-8-544 therapy blocks | Kaplan-Meier — publication-ready | Oncoprint table | Launching the dashboard
Rendered fromzhncommandR.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-06-16

The Shiny dashboard
Launching | Layout | Figures: transparency and export | The Kaplan-Meier tab | Privacy
Rendered fromshiny-app.Rmdusingknitr::rmarkdown

Last update: 2026-10-28
Started: 2026-06-16

Readme and manuals

Help Manual

Help pageTopics
Cohort data framenew_cohort_df
Diagnostic-blocks data framenew_diagnostic_blocks
Therapy-blocks data framenew_therapy_blocks
Classify a free-text alteration stringzhn_alteration_type
Path to the bundled synthetic example workbookzhn_example_path
Logical: should this alteration class appear in the oncoprint?zhn_is_mutation
Pairwise log-rank comparisons with Benjamini-Hochberg correctionzhn_km_pairwise
Normalise a free-text alteration labelzhn_normalize_alteration
zhncommandR figure palettezhn_pal
Parse the cytogenetics free-text columnzhn_parse_cytogenetics
Parse the oncoprint free-text mutation columnzhn_parse_oncoprint
Figure: cases per treatment year (vertical bar)zhn_plot_cases_by_year
Figure: top diagnoses / codings (horizontal bar)zhn_plot_diagnoses
Publication-ready Kaplan-Meier plot (ggsurvfit)zhn_plot_km
Prepare OPS-1-941 complex-diagnostics blockszhn_prepare_diagnostic_blocks
Prepare OPS-8-544 therapy blocks for downstream analysiszhn_prepare_therapy_blocks
Read the cohort sheet (Basisdaten / Faelle)zhn_read_cohort
Read the OPS-1-941 (complex diagnostics) sheetzhn_read_diagnostics
Read the OPS-8-544 (complex chemotherapy) sheetzhn_read_therapy
Read previously exported tumour-board decisionszhn_read_tumorboard
Register the bundled Inter font for live display and exportszhn_register_fonts
Launch the zhncommandR Shiny dashboardzhn_run_app
Save a zhncommandR figure to PNG (600 dpi) or PDF (vector)zhn_save_plot
zhncommandR figure theme (Hugo Coder look)zhn_theme