Pass values to setup function and the global environment will be arranged for use reporting tools.

Usage

rs_setup(
  R_DICTION = "./inst/formats",
  R_MACDIRS = NULL,
  R_DDDATA = NULL,
  R_OTHERDATA = paste0("./data"),
  R_INPUTDATA = paste0("./data"),
  R_RAWDATA = paste0("./data"),
  R_SDTMDATA = paste0("./data"),
  R_ADAMDATA = paste0("./data"),
  R_RFMTDIR = paste0("./inst/formats"),
  D_CENTID = "SITEID",
  D_DATADATE = NULL,
  D_DSPLYNUM = 1,
  D_DSPLYTYP = "T",
  D_FONTSIZE = 10,
  D_KEEPPOPVARS = NULL,
  D_OUTFILE = "./inst/t_ru_list_1.rtf",
  D_PGMPTH = "./R/rs_setup.R",
  D_STUDYID = NULL,
  D_STUDY_DESC = NULL,
  D_POP = "ITTEFL",
  D_POPDATA = NULL,
  D_POPLBL = "Intent-to-Treat",
  D_SUBJID = "USUBJID",
  D_SUBPOP = NULL,
  D_SUBSET = NULL,
  D_TITLE1 = NULL,
  D_TITLE2 = NULL,
  D_TITLE3 = NULL,
  D_TITLE4 = NULL,
  D_TITLE5 = NULL,
  D_TITLE6 = NULL,
  D_TITLE7 = NULL,
  D_FOOT1 = NULL,
  D_FOOT2 = NULL,
  D_FOOT3 = NULL,
  D_FOOT4 = NULL,
  D_FOOT5 = NULL,
  D_FOOT6 = NULL,
  D_FOOT7 = NULL,
  D_FOOT8 = NULL,
  D_FOOT9 = NULL,
  D_USERID = Sys.getenv("USERNAME"),
  D_RTFYN = "N",
  D_DEBUG = 0,
  RetEnv = FALSE
)

Arguments

R_DICTION: Location of reporting dictionaries.
R_MACDIRS: List of folders to search for functions when they are invoked.
R_DDDATA: Location to write DDDATA reporting data sets.
R_OTHERDATA: Location of additional production data sets.
R_INPUTDATA: Location of permanent formats data sets and miscellaneous data sets.
R_RAWDATA: Location of raw data sets.
R_SDTMDATA: Location of SDTM data sets.
R_ADAMDATA: Location of ADAM data sets.
R_RFMTDIR: Location of format catalogs and corresponding lists.
D_CENTID: Variable name for investigational center.
D_DATADATE: Date of data sets for use in titles/footnotes.
D_DSPLYNUM: Display number for title.
D_DSPLYTYP: Type of Display ('T','L','F').
D_FONTSIZE: Size of font on output file which is RTF by default (with automated PDF conversion via script).
D_KEEPPOPVARS: Variables to keep on the population data set when merging to apply populations and sub-populations.
D_OUTFILE: Production location for output TLFs.
D_PGMPTH: Path of the driver file that generates current outputs or data sets.
D_STUDYID: Protocol ID for the study.
D_STUDY_DESC: Description of Study.
D_POP: Population variable from ADSL that must equal Y for subjects to be included in the analysis.
D_POPDATA: Data set that contains the population to be analyzed.
D_POPLBL: Label for population being analyzed which can be used in the TLF header.
D_SUBJID: The variable used to uniquely identify a subject in this analysis.
D_SUBPOP: Condition to identify the sub-population when applied to ADSL.
D_SUBSET: Condition to filter data from incoming source data sets used for this TLF.
D_TITLE1: First title text.
D_TITLE2: Second title text.
D_TITLE3: Third title text.
D_TITLE4: Fourth title text.
D_TITLE5: Fifth title text.
D_TITLE6: Sixth title text.
D_TITLE7: Seventh title text.
D_FOOT1: First footnote text.
D_FOOT2: Second footnote text.
D_FOOT3: Third footnote text.
D_FOOT4: Fourth footnote text.
D_FOOT5: Fifth footnote text.
D_FOOT6: Sixth footnote text.
D_FOOT7: Seventh footnote text.
D_FOOT8: Eighth footnote text.
D_FOOT9: Ninth footnote text.
D_USERID: User name.
D_RTFYN: Y or N to generate RTf output.
D_DEBUG: Level of debugging to show in log files.
RetEnv: Return environment variable containing current settings.

Value

'NULL' because variables defined for use with the reporting tools.

Author

Yongwei Wang, yongwei.x.wang@viivhealthcare.com
Chris Rook, cr883296@gmail.com

Examples

library(repfun)
library(dplyr)
#> 
#> Attaching package: ‘dplyr’
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
datdir <- file.path(gsub("\\","/",tempdir(),fixed=TRUE),"datdir")
dir.create(datdir,showWarnings=FALSE)
outdir <- file.path(gsub("\\","/",tempdir(),fixed=TRUE),"outdir")
dir.create(outdir,showWarnings=FALSE)
fmtdir <- file.path(gsub("\\","/",tempdir(),fixed=TRUE),"fmtdir")
dir.create(fmtdir,showWarnings=FALSE)
repfun::copydata(datdir)
repfun::rs_setup(
D_CENTID="SITEID",
D_DATADATE=Sys.Date(),
D_DSPLYNUM=1,
D_DSPLYTYP='T',
D_FONTSIZE=10,
D_FOOT1='1.) Only treatment emergent events related to lipids are displayed.',
D_FOOT2='2.) Subjects are counted once in each body system & preferred term.',
D_KEEPPOPVARS=c('STUDYID','USUBJID','SAFFL'),
D_USERID=Sys.getenv("USERNAME"),
D_STUDYID='ABCXYZPDQ',
D_POP="SAFFL",
D_POPDATA=repfun::adsl %>% dplyr::filter(SAFFL=='Y'),
D_POPLBL="Safety",
D_SUBJID=c("STUDYID","USUBJID"),
D_TITLE1=paste0('Table 1: Summary of Treatment Emergent Adverse Events'),
D_RTFYN="Y",
D_DEBUG=0,
R_DICTION=NULL,
R_OTHERDATA=NULL,
R_INPUTDATA=NULL,
R_RAWDATA=NULL,
R_SDTMDATA=NULL,
R_ADAMDATA=datdir,
R_RFMTDIR=fmtdir,
R_DDDATA=paste0(outdir,'/t_ru_list_1.rds'),
D_OUTFILE=paste0(outdir,"/t_ru_list_1.rtf"),
D_PGMPTH="/path/to/code/rs_setup.R")