Package: clinUtils 0.2.0

Laure Cougnaud

clinUtils: General Utility Functions for Analysis of Clinical Data

Utility functions to facilitate the import, the reporting and analysis of clinical data. Example datasets in 'SDTM' and 'ADaM' format, containing a subset of patients/domains from the 'CDISC Pilot 01 study' are also available as R datasets to demonstrate the package functionalities.

Authors:Laure Cougnaud [aut, cre], Michela Pasetto [aut], Arne De Roeck [rev], Open Analytics [cph]

clinUtils_0.2.0.tar.gz
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clinUtils.pdf |clinUtils.html✨
clinUtils/json (API)
NEWS

# Install 'clinUtils' in R:

install.packages('clinUtils', repos = c('https://openanalytics.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/openanalytics/clinutils/issues

Datasets:

colorPaletteNRIND - Color palette for a standard CDISC Normal/Reference Range Indicator.
dataADaMCDISCP01 - Example of ADaM datasets from the CDISC original Pilot 01 study
dataSDTMCDISCP01 - Example of SDTM datasets from the CDISC original Pilot 01 study
shapePaletteNRIND - Shape palette for a standard CDISC Normal/Reference Range Indicator.

On CRAN:

30 exports 3 stars 1.92 score 59 dependencies 3 dependents 104 scripts 1.3k downloads

Last updated 4 months agofrom:271fbd6f79. Checks:OK: 5 NOTE: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 14 2024
R-4.5-win	NOTE	Sep 14 2024
R-4.5-linux	NOTE	Sep 14 2024
R-4.4-win	OK	Sep 14 2024
R-4.4-mac	OK	Sep 14 2024
R-4.3-win	OK	Sep 14 2024
R-4.3-mac	OK	Sep 14 2024

Exports:clinColors clinLinetypes clinShapes clinShapesText compareDiff compareTables convertToDateTime exportDiffData formatLabel formatLabelChunk formatLongLabel formatTableLabel formatVarForPlotLabel getClinDT getClinDTButtons getColorPalette getLabelParamcd getLabelVar getLabelVars getLinetypePalette getPaletteCDISC getShapePalette knitPrintListObjects knitPrintListPlots loadDataADaMSDTM mergeDiffWithData reorderColumns roundHalfUp roundHalfUpTextFormat simpleCap

Dependencies:base64enc bit bit64 bslib cachem cli clipr cpp11 crayon crosstalk data.table digest DT evaluate fansi fastmap fontawesome forcats fs glue haven highr hms htmltools htmlwidgets httpuv jquerylib jsonlite knitr later lazyeval lifecycle magrittr memoise mime pillar pkgconfig plyr prettyunits progress promises R6 rappdirs Rcpp readr rlang rmarkdown sass tibble tidyselect tinytex tzdb utf8 vctrs viridisLite vroom withr xfun yaml

Introduction to the clinUtils package

Laure Cougnaud and Michela Pasetto

Rendered fromclinUtils-vignette.Rmdusingknitr::rmarkdownon Sep 14 2024.

Last update: 2022-02-01
Started: 2022-02-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check if specified variables are in the data. If they are not, they are removed from specified variables and a message is printed.	checkVarInData
Colors of 'clinUtils'	clinColors
Linetypes of 'clinUtils'	clinLinetypes
Shapes of 'clinUtils'	clinShapes
Shapes of 'clinUtils' as text	clinShapesText
Parameters for all palette functions for clinical visualizations.	clinUtils-palette
Color palette for a standard CDISC Normal/Reference Range Indicator.	colorPaletteNRIND
Get differences between two data.frames	compareDiff
Compare tables	compareTables
General parameters used for the comparison table functionality	comparisonTables-common-args
Convert to data.table	convertToDatatable
Convert character vector to date/time object	convertToDateTime
Example of ADaM datasets from the CDISC original Pilot 01 study	dataADaMCDISCP01
Example of SDTM datasets from the CDISC original Pilot 01 study	dataSDTMCDISCP01
Export the 'diff.data' object from 'compareDiff' to a user-friendly format	exportDiffData
Format details comparison	formatDetailsComparison
Format a variable in a 'datatable' as a barplot.	formatDTBarVar
Concatenate and format text strings to a label	formatLabel
Concatenate and format text strings to a chunk label	formatLabelChunk
Format a variable with long labels	formatLongLabel
Concatenate and format text strings to a label of a table	formatTableLabel
Format parameter variable to be displayed in the labels of a plot	formatVarForPlotLabel
Create an interactive table to display clinical data	getClinDT
Get a default set of buttons to be included in the interactive table for clinical data.	getClinDTButtons
Get a color palette for clinical visualizations.	getColorPalette
Get label for a parameter code	getLabelParamcd
Get label for a variable of the dataset	getLabelVar
Get label of the variables in SAS dataset(s)	getLabelVars
Get a linetype palette for clinical visualizations.	getLinetypePalette
Get standard palette for typical CDISC variables.	getPaletteCDISC
Get additions/removals	getSetDiff
Get a shape palette for clinical visualizations.	getShapePalette
Include a list of objects in a knitr document	knitPrintListObjects
Include a list of plots in a knitr document	knitPrintListPlots
Load data from ADaM/SDTM file(s).	loadDataADaMSDTM
Merge the 'diff.data' object from 'compareDiff' with the original 'newData' or 'oldData'.	mergeDiffWithData
Custom merge of difference data with input data	mergeInputDiff
Function for reordering columns	reorderColumns
Round a number with 'rounding up' strategy for rounding off a 5	roundHalfUp
Round a number with 'round-up' strategy for rounding off a 5 in text format	roundHalfUpTextFormat
Shape palette for a standard CDISC Normal/Reference Range Indicator.	shapePaletteNRIND
Capitalize the first letter of a word/sentence.	simpleCap