Package: BiostatsUHNplus 1.0.4

BiostatsUHNplus: Nested Data Summary, Adverse Events and REDCap

Tools and code snippets for summarizing nested data, adverse events and REDCap study information.

Authors:Lisa Avery [aut], Zeynep Baskurt [aut], Osvaldo Espin-Garcia [aut], Katrina Hueniken [aut], Katherine Lajkosz [aut], Xuan Li [aut], Tyler Pittman [cre, aut], Anna Santiago [aut], Jessica Weiss [aut], Wei Xu [aut]

BiostatsUHNplus_1.0.4.tar.gz
BiostatsUHNplus_1.0.4.zip(r-4.7-any)BiostatsUHNplus_1.0.4.zip(r-4.6-any)BiostatsUHNplus_1.0.4.zip(r-4.5-any)
BiostatsUHNplus_1.0.4.tgz(r-4.6-any)BiostatsUHNplus_1.0.4.tgz(r-4.5-any)
BiostatsUHNplus_1.0.4.tar.gz(r-4.7-any)BiostatsUHNplus_1.0.4.tar.gz(r-4.6-any)
BiostatsUHNplus_1.0.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
BiostatsUHNplus/json (API)

# Install 'BiostatsUHNplus' in R:
install.packages('BiostatsUHNplus', repos = c('https://tylerpittman.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • ae - Simulated adverse events for patients receiving two study agents.
  • demography - Simulated demography for patients.
  • drug1_admin - Simulated study agent 1 for patients.
  • drug2_admin - Simulated study agent 2 for patients.
  • enrollment - Enrollment data Simulated enrollment for patients.
  • ineligibility - Simulated ineligibility for patients.

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 10 scripts 289 downloads 10 exports 134 dependencies

Last updated from:41c0fe69f5. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK241
source / vignettesOK238
linux-release-x86_64OK225
macos-release-arm64OK160
macos-oldrel-arm64OK171
windows-develOK161
windows-releaseOK169
windows-oldrelOK151
wasm-releaseOK162

Exports:ae_timeline_plotas_numeric_parsecaterpillar_plotdsmb_ccrudsmb_ddpnice_mcmcglmmnice_mcmcglmm_iccredcap_data_outrm_ae_all_g3prm_covsum_nested

Dependencies:abindafexaodapebackportsbase64encbootbroombslibcachemcarcarDatacliclueclustercmprskcodacolorspacecorpcorcorrplotcowplotcpp11cubatureDerivdigestdoBydplyrevaluatefarverfastmapfBasicsfontawesomeforcatsforecastFormulafracdifffsgenericsggh4xggplot2ggpubrggrepelggsciggsignifgluegridExtragssgtablehighrhtmltoolsisobandjquerylibjsonlitekableExtraknitrlabelinglatticelifecyclelme4lmerTestlmtestmagrittrMASSMatrixMatrixModelsMCMCglmmmemoisemgcvmimeminqamodeestmodelrnlmenloptrnnetnumDerivopenxlsxpanderparallellypbkrtestpillarpkgconfigplyrpolynompurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasreportRmdreshape2rlangrmarkdownrmutilrpartrstatixrstudioapiS7sassscalesSparseMspatialstablestablediststatipstringistringrsurvivalsvglitesystemfontstensorAtextshapingtibbletidyrtidyselecttimeDatetimeSeriestinytexurcautf8vctrsviridisLitewithrxfunxml2yamlzipzoo

Readme and manuals

Help Manual

Help pageTopics
Simulated adverse events for patients receiving two study agents.ae
Outputs related adverse event timeline plots including just system organ class (AE category), or system organ class and lowest level term (AE detail). This function can fit up to 5 different attributions. Modify width, height and scale parameters in ggsave() to customize fit for large plot.ae_timeline_plot
Modification of the as.numeric function that prints entries that fail to parse as a messageas_numeric_parse
Caterpillar plot. Useful for plotting random effects from hierarchical models, such as MCMCglmm::MCMCglmm() object, that have binary outcome.caterpillar_plot
Nested version of reportRmd covsum()covsum_nested
Simulated demography for patients.demography
Simulated study agent 1 for patients.drug1_admin
Simulated study agent 2 for patients.drug2_admin
Outputs the three DSMB-CCRU AE summary tables in Excel format per UHN templatedsmb_ccru
Outputs the DSMB-DDP AE summary tables in Excel format per UHN templatedsmb_ddp
Enrollment data Simulated enrollment for patients.enrollment
Simulated ineligibility for patients.ineligibility
Nice table of model output from MCMCglmm::MCMCglmm()nice_mcmcglmm
Nice table of intraclass correlation coefficients from MCMCglmm::MCMCglmm() model outputnice_mcmcglmm_icc
Combines exported REDCap raw and label .csv files together with data dictionary. Tranforms the exported data into Excel sheets by survey instrument with one row per participantredcap_data_out
Outputs R Markdown table of all and grade 3+ adverse events by comparison grouprm_ae_all_g3p
Outputs a nested version of reportRmd::rm_covsum()rm_covsum_nested