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clinUtils (version 0.1.4)

General Utility Functions for Analysis of Clinical Data

Description

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.

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Install

install.packages('clinUtils')

Monthly Downloads

818

Version

0.1.4

License

MIT + file LICENSE

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Repository

https://github.com/openanalytics/clinUtils

Maintainer

Laure Cougnaud

Last Published

January 6th, 2023

Functions in clinUtils (0.1.4)

Export the 'diff.data' object from compareDiff to a user-friendly format

Get differences between two data.frames

Format a variable in a datatable as a barplot.

knitPrintListObjects

Include a list of objects in a knitr document

formatDetailsComparison

Format details comparison

convertToDatatable

Convert to data.table

formatLabelChunk

Concatenate and format text strings to a chunk label

dataADaMCDISCP01

Example of ADaM datasets from the CDISC original Pilot 01 study

Concatenate and format text strings to a label

getColorPalette

Get a color palette for clinical visualizations.

formatLongLabel

Format a variable with long labels

convertToDateTime

Convert character vector to date/time object

Get label of the variables in SAS dataset(s)

Custom merge of difference data with input data

Get label for a variable of the dataset

knitPrintListPlots

Include a list of plots in a knitr document

dataSDTMCDISCP01

Example of SDTM datasets from the CDISC original Pilot 01 study

getLinetypePalette

Get a linetype palette for clinical visualizations.

getPaletteCDISC

Get standard palette for typical CDISC variables.

Get additions/removals

shapePaletteNRIND

Shape palette for a standard CDISC Normal/Reference Range Indicator.

formatTableLabel

Concatenate and format text strings to a label of a table

getShapePalette

Get a shape palette for clinical visualizations.

Capitalize the first letter of a word/sentence.

formatVarForPlotLabel

Format parameter variable to be displayed in the labels of a plot

getLabelParamcd

Get label for a parameter code

Create an interactive table to display clinical data

getClinDTButtons

Get a default set of buttons to be included in the interactive table for clinical data.

Function for reordering columns

Round a number with 'rounding up' strategy for rounding off a 5

loadDataADaMSDTM

Load data from ADaM/SDTM file(s).

roundHalfUpTextFormat

Round a number with 'round-up' strategy for rounding off a 5 in text format

mergeDiffWithData

Merge the 'diff.data' object from compareDiff with the original newData or oldData.

Linetypes of 'clinUtils'

Check if specified variables are in the data. If they are not, they are removed from specified variables and a message is printed.

Colors of 'clinUtils'

comparisonTables-common-args

General parameters used for the comparison table functionality

clinUtils-palette

Parameters for all palette functions for clinical visualizations.

Shapes of 'clinUtils' as text

colorPaletteNRIND

Color palette for a standard CDISC Normal/Reference Range Indicator.

Shapes of 'clinUtils'