Package: bstfun 0.5.1

Karissa Whiting

bstfun: Functions for the MSK Biostatistics Department

A miscellaneous collection of functions to used by members of the Biostatistics Department at MSKCC.

Authors:Karissa Whiting [aut, cre], Daniel D. Sjoberg [aut, ccp], Jessica A. Lavery [aut], Margie Hannum [ctb], Meier Hsu [ctb], Caroline Kostrzewa [ctb], Jasme Lee [ctb], Amy Tin [ctb], Emily Vertosick [ctb], Gustavo Zapata Wainberg [ctb], Christine Zhou [ctb], Stephanie Lobaugh [ctb]

bstfun_0.5.1.tar.gz
bstfun_0.5.1.zip(r-4.5)bstfun_0.5.1.zip(r-4.4)bstfun_0.5.1.zip(r-4.3)
bstfun_0.5.1.tgz(r-4.4-any)bstfun_0.5.1.tgz(r-4.3-any)
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bstfun.pdf |bstfun.html✨
bstfun/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/mskcc-epi-bio/bstfun/issues

Datasets:
  • project_templates - Biostatistics project templates
  • trial - Results from a simulated study of two chemotherapy agents: Drug A and Drug B

On CRAN:

4.87 score 34 stars 31 scripts 74 exports 100 dependencies

Last updated 2 years agofrom:826b39f4dc (on v0.5.1). Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winERROROct 31 2024
R-4.5-linuxERROROct 31 2024
R-4.4-winERROROct 31 2024
R-4.4-macERROROct 31 2024
R-4.3-winERROROct 31 2024
R-4.3-macERROROct 31 2024

Exports:%>%add_continuous_statadd_cuminc_risktableadd_inline_forest_plotadd_nadd_sparklineadd_splinesadd_variable_groupingall_ofany_ofas_forest_plotas_ggplotas_gtas_kableassign_timepointauc_densityauc_histogrambold_italicize_group_labelscite_rclean_mrncontainscount_mapcount_nacreate_bst_projectcreate_hot_projectegfr_ckdepiegfr_mdrdends_witheverythingfix_database_errorfollowup_timeget_data_dateget_modeggcalibrationgts_add_p_footnotesgtsummary_butcherherehere_datahpcc_get_arghpcc_get_seq_numberlast_collist_labelslogistic_reg_adj_diffmatchesnum_rangeone_ofpath_datareinstall_prior_pkgsrm_logsset_derived_variablesstarts_withstyle_percentstyle_pvaluestyle_ratiostyle_sigfigstyle_tbl_compacttbl_2way_summarytbl_likerttbl_splittheme_gtsummary_mskuse_bst_analysisuse_bst_fileuse_bst_gitignoreuse_bst_readmeuse_bst_reportuse_bst_rstudio_prefsuse_bst_setupuse_hot_analysisuse_hot_fileuse_hot_gitignoreuse_hot_readmeuse_hot_reportuse_hot_setupuse_varnames_as_labels

Dependencies:askpassbackportsbase64encbigDbitbit64bitopsbroombroom.helpersbslibcachemcardsclicliprcolorspacecommonmarkcpp11crayoncredentialscurldigestdplyrevaluatefansifarverfastmapfontawesomeforcatsfsgenericsgertgluegtgtsummaryhavenherehighrhmshtmltoolshtmlwidgetshttrjquerylibjsonlitejuicyjuiceknitrlabelinglabelledlifecyclelubridatemagrittrmarkdownmemoisemimemunsellopensslpillarpkgconfigprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppreactablereactRreadrrenvrlangrmarkdownrprojrootrstudio.prefsrstudioapirvestsassscalesselectrstarterstringistringrsystibbletidyrtidyselecttimechangetinytextzdbutf8V8vctrsviridisLitevroomwithrxfunxml2yamlzip

Readme and manuals

Help Manual

Help pageTopics
Add risk table to 'cuminc()' plotadd_cuminc_risktable
Add inline forest plotadd_inline_forest_plot
Add Sparkline Figureadd_sparkline
Add spline terms to a data frameadd_splines
Group variable summariesadd_variable_grouping
Create Forest Plotas_forest_plot
Convert gt/gtsummary table to ggplotas_ggplot
Assign a time point to a long data set with multiple measuresassign_timepoint
Calculate exact AUCs based on the distribution of risk in a populationauc auc_density auc_histogram
Set bold and/or italic style for groups labels in stacked tablesbold_italicize_group_labels
Cite R and R Packagescite_r
Check and Format MRNsclean_mrn
Check variable derivationscount_map
Assess pattern of missing datacount_na
Start a New Biostatistics projectcreate_bst_project create_project
Calculate eGFRegfr egfr_ckdepi egfr_mdrd
Function to make database fixes after importfix_database_error
Report Follow-up Among Censored Obsfollowup_time
Calculates the mode(s) of a set of valuesget_mode
Model Calibration Plotggcalibration
Find your data folderget_data_date here_data path_data
HPCC Functionshpcc hpcc_get_arg hpcc_get_seq_number
Get variable labels and store in named listlist_labels
Logistic regression adjusted differenceslogistic_reg_adj_diff
Biostatistics project templatesproject_templates
Deletes log files created by Rscript on the Linux clusterrm_logs
Apply variable labels to data frameset_derived_variables
Compact Table Stylingstyle_tbl_compact
Likert Summary Tableadd_continuous_stat add_continuous_stat.tbl_likert add_n.tbl_likert tbl_likert
Set custom gtsummary themestheme_gtsummary_msk
Results from a simulated study of two chemotherapy agents: Drug A and Drug Btrial
Use Biostatistics RStudio Preferencesuse_bst_rstudio_prefs
Write a template fileuse_bst_analysis use_bst_file use_bst_gitignore use_bst_readme use_bst_report use_bst_setup use_file
Use Variable Names as Labelsuse_varnames_as_labels