Package: reportRmd 0.1.0

Lisa Avery

reportRmd: Tidy Presentation of Clinical Reporting

Streamlined statistical reporting in 'Rmarkdown' environments. Facilitates the automated reporting of descriptive statistics, multiple univariate models, multivariable models and tables combining these outputs. Plotting functions include customisable survival curves, forest plots from logistic and ordinal regression and bivariate comparison plots.

Authors:Lisa Avery [cre, aut], Ryan Del Bel [aut], Osvaldo Espin-Garcia [aut], Katherine Lajkosz [aut], Tyler Pittman [aut], Anna Santiago [aut], Yanning Wang [ctr], Jessica Weiss [aut], Wei Xu [aut]

reportRmd_0.1.0.tar.gz
reportRmd_0.1.0.tar.gz(r-4.5-noble)reportRmd_0.1.0.tar.gz(r-4.4-noble)
reportRmd_0.1.0.tgz(r-4.4-emscripten)reportRmd_0.1.0.tgz(r-4.3-emscripten)
reportRmd.pdf |reportRmd.html✨
reportRmd/json (API)
NEWS

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

Peer review:

Datasets:
  • ctDNA - Tumour size change over time Longitudinal changes in tumour size since baseline for patients by changes in ctDNA status (clearance, decrease or increase) since baseline.
  • pembrolizumab - Survival data Survival status and ctDNA levels for patients receiving pembrolizumab
  • testData - Funky ctDNA data There is a weird factor with all one level, the cohort variable contains a cohort level (and Cohort A) and for one cohort all the size changes are missing

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

25 exports 0.36 score 98 dependencies 1 dependents 21 scripts 222 downloads

Last updated 10 months agofrom:bdceec7192. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-linuxNOTESep 12 2024

Exports:clear_labelscrrRxexcelColexcelColLettersextract_labelsforestplot2forestplotMVforestplotUVforestplotUVMVggkmcifggkmcif_pasteggkmcif2nestTableoutTableplotuvrm_cifsumrm_covsumrm_mvsumrm_survdiffrm_survsumrm_survtimerm_uv_mvrm_uvsumset_labelsset_var_labels

Dependencies:abindaodbackportsbase64encbootbroombslibcachemcarcarDataclicmprskcolorspacecorrplotcowplotcpp11DerivdigestdoBydplyrevaluatefansifarverfastmapfontawesomefsgeepackgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtablehighrhtmltoolsisobandjquerylibjsonlitekableExtraknitrlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivpanderpbkrtestpillarpkgconfigplyrpolynompurrrquantregR6rappdirsRColorBrewerRcppRcppEigenrlangrmarkdownrstatixrstudioapisassscalesSparseMstringistringrsurvivalsvglitesystemfontstibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxml2yaml

reportRmd Package

Rendered fromreportRmd.Rmdusingknitr::rmarkdownon Sep 12 2024.

Last update: 2023-11-17
Started: 2022-10-17

Readme and manuals

Help Manual

Help pageTopics
Add spaces to strings in LaTeXaddspace
fit box cox transformed linear modelboxcoxfitRx
Capitalize a stringcap
Clear variable labels from a data frameclear_labels
Get covariate summary dataframecovsum
fit crr modelcrrRx
Tumour size change over time Longitudinal changes in tumour size since baseline for patients by changes in ctDNA status (clearance, decrease or increase) since baseline.ctDNA
Retrieve columns number from spreadsheet columns specified as unquoted lettersexcelCol
Retrieve spreadsheet column letter-names from columns indicesexcelColLetters
Extract variable labels from labelled data frameextract_labels
Create a forest plot using ggplot2forestplot2
Create a multivariable forest plot using ggplot2forestplotMV
Create an univariable forest plot using ggplot2forestplotUV
Combine an univariable and multivariable forest plot using ggplot2forestplotUVMV
Specific p-value formattingformatp
Parameter Estimation for the Box-Cox TransformationgeoR_boxcoxfit
Plot KM and CIF curves with ggplotggkmcif
Plot KM and CIF curves with ggplotggkmcif_paste
Plot KM and CIF curves with ggplotggkmcif2
Additional parameters passed to ggkmcif2ggkmcif2Parameters
Bold strings in HTMLhbld
Bold strings in LaTeXlbld
Formats p-values for LaTeXlpvalue
Get multivariate summary dataframemvsum
Combine two table columns into a single column with levels of one nested within levels of the other.nestTable
Lean strings for printingnicename
Round retaining digitsniceNum
Print tables to PDF/Latex HTML or WordoutTable
Survival data Survival status and ctDNA levels for patients receiving pembrolizumabpembrolizumab
Plot multiple bivariate relationships in a single plotplotuv
Round and paste with parenthesespsthr
Paste with parenthesespstprn
Formats p-valuespvalue
Summarize cumulative incidence by grouprm_cifsum
Outputs a descriptive covariate tablerm_covsum
Format a regression model nicely for 'Rmarkdown'rm_mvsum
Display event counts, expected event counts and logrank test of differencesrm_survdiff
Summarise survival data by grouprm_survsum
Display survival rates and events for specified timesrm_survtime
Combine univariate and multivariable regression tablesrm_uv_mv
Output several univariate models nicely in a single tablerm_uvsum
Replace dollar signs with html for proper HTML outputrmds
Sanitizes strings to not break LaTeXsanitizestr
Set variable labelsset_labels
Set variable labelsset_var_labels
Funky ctDNA data There is a weird factor with all one level, the cohort variable contains a cohort level (and Cohort A) and for one cohort all the size changes are missingtestData
Get univariate summary dataframeuvsum