inTextSummaryTable packageThe package inTextSummaryTable contains functionalities to create complex table of summary statistics or counts of variables of interest.
This table can be formatted to static
These tables can be included into a rmarkdown document which can be converted into html, docx and pptx. Each table can be separately exported into a text, docx or htmldocument.
We start the guidance to the functionalities of the inTextSummaryTable, via loading the following packages.
library(inTextSummaryTable)
library(pander)
library(tools) # toTitleCaseThe input data for the creation of summary table should be a data.frame, usually loaded from a SAS data file (sas7bdat format). The label of the variables stored in the SAS datasets is also used for the title or the caption.
Note that the loadDataADaMSDTM function of the clinUtils package can be used to import your study-specific dataset(s) of interest into R.
For this vignette, ADaM datasets included in the clinUtils package are used.
library(clinUtils)
# load example data
data(dataADaMCDISCP01)
dataAll <- dataADaMCDISCP01
labelVars <- attr(dataAll, "labelVars")
# dataAll contains a list
class(dataAll)## [1] "list" # ... of ADaM datasets
names(dataAll)## [1] "ADAE" "ADCM" "ADLBC" "ADPP" "ADQSADAS" "ADQSCIBC" "ADSL" "ADVS" # access a specific dataset
head(dataAll$ADSL, 1)## STUDYID USUBJID SUBJID SITEID SITEGR1 ARM TRT01P TRT01PN TRT01A TRT01AN TRTSDT TRTEDT TRTDUR AVGDD
## 1 CDISCPILOT01 01-701-1148 1148 701 701 Xanomeline High Dose Xanomeline High Dose 81 Xanomeline High Dose 81 2013-08-23 2014-02-20 182 77.1
## CUMDOSE AGE AGEGR1 AGEGR1N AGEU RACE RACEN SEX ETHNIC SAFFL ITTFL EFFFL COMP8FL COMP16FL COMP24FL DISCONFL DSRAEFL DTHFL BMIBL BMIBLGR1 HEIGHTBL
## 1 14040 57 <65 1 YEARS WHITE 1 M NOT HISPANIC OR LATINO Y Y Y Y Y Y 28.3 25-<30 175.3
## WEIGHTBL EDUCLVL DISONSDT DURDIS DURDSGR1 VISIT1DT RFSTDTC RFENDTC VISNUMEN RFENDT DCDECOD DCREASCD MMSETOT DATASET
## 1 87.1 15 2010-12-12 32.1 >=12 2013-08-14 2013-08-23 2014-02-20 12 2014-02-20 COMPLETED Completed 21 ADSL # check label of a subset of the variable(s)
head(labelVars)## STUDYID SITEID USUBJID TRTA TRTAN AGE
## "Study Identifier" "Study Site Identifier" "Unique Subject Identifier" "Actual Treatment" "Actual Treatment (N)" "Age" # or for a specific variable:
labelVars["USUBJID"]## USUBJID
## "Unique Subject Identifier" # or:
getLabelVar(var = "USUBJID", labelVars = labelVars)## USUBJID
## "Unique Subject Identifier"A dedicated vignette on how to create your in-text table is available here).
If you are familiar with the creation of the tables, but you are wondering how to:
then the the dedicated vignette is available here), or accessible with
vignette("inTextSummaryTable-exportTables", "inTextSummaryTable")If you are familiar with the creation and export of the tables, and you want to know more on the functionalities less exposed to the users, you can check out the vignette for advanced users, which is available here) and with
vignette("inTextSummaryTable-advanced", "inTextSummaryTable")The inTextSummaryTable has also visualization functionalities based on the computation of summary statistics. The vignette for visualization is available at this) link or through
vignette("inTextSummaryTable-visualization", "inTextSummaryTable")The inTextSummaryTable package allow the user to set global options for the color schemes of tables and visualization. The main advantage is that if you wish to change the default palettes, it is possible to set your preferences only once at the beginning of the R script or Rmd document.
The vignette is available via this) link or
vignette("inTextSummaryTable-aesthetics", "inTextSummaryTable")R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
locale: LC_CTYPE=en_US.UTF-8, LC_NUMERIC=C, LC_TIME=en_US.UTF-8, LC_COLLATE=C, LC_MONETARY=en_US.UTF-8, LC_MESSAGES=en_US.UTF-8, LC_PAPER=en_US.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.UTF-8 and LC_IDENTIFICATION=C
attached base packages: tools, stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: plyr(v.1.8.9), pander(v.0.6.5), clinUtils(v.0.1.4), inTextSummaryTable(v.3.3.2) and knitr(v.1.45)
loaded via a namespace (and not attached): gtable(v.0.3.4), xfun(v.0.42), bslib(v.0.6.1), ggplot2(v.3.5.0), htmlwidgets(v.1.6.4), ggrepel(v.0.9.5), vctrs(v.0.6.5), crosstalk(v.1.2.1), generics(v.0.1.3), curl(v.5.2.1), tibble(v.3.2.1), fansi(v.1.0.6), highr(v.0.10), pkgconfig(v.2.0.3), data.table(v.1.15.2), uuid(v.1.2-0), lifecycle(v.1.0.4), flextable(v.0.9.5), farver(v.2.1.1), stringr(v.1.5.1), compiler(v.4.3.3), textshaping(v.0.3.7), munsell(v.0.5.0), httpuv(v.1.6.14), fontquiver(v.0.2.1), fontLiberation(v.0.1.0), htmltools(v.0.5.7), sass(v.0.4.8), yaml(v.2.3.8), later(v.1.3.2), pillar(v.1.9.0), crayon(v.1.5.2), jquerylib(v.0.1.4), gfonts(v.0.2.0), ellipsis(v.0.3.2), openssl(v.2.1.1), DT(v.0.32), cachem(v.1.0.8), mime(v.0.12), fontBitstreamVera(v.0.1.1), tidyselect(v.1.2.0), zip(v.2.3.1), digest(v.0.6.34), stringi(v.1.8.3), reshape2(v.1.4.4), dplyr(v.1.1.4), labeling(v.0.4.3), forcats(v.1.0.0), cowplot(v.1.1.3), fastmap(v.1.1.1), grid(v.4.3.3), colorspace(v.2.1-0), cli(v.3.6.2), magrittr(v.2.0.3), crul(v.1.4.0), utf8(v.1.2.4), withr(v.3.0.0), gdtools(v.0.3.7), scales(v.1.3.0), promises(v.1.2.1), rmarkdown(v.2.26), officer(v.0.6.5), askpass(v.1.2.0), ragg(v.1.2.7), hms(v.1.1.3), shiny(v.1.8.0), evaluate(v.0.23), haven(v.2.5.4), viridisLite(v.0.4.2), rlang(v.1.1.3), Rcpp(v.1.0.12), xtable(v.1.8-4), glue(v.1.7.0), httpcode(v.0.3.0), xml2(v.1.3.6), jsonlite(v.1.8.8), R6(v.2.5.1) and systemfonts(v.1.0.6)