repfun (version 0.1.2)

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

Description

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
)

Value

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

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.

Author

Yongwei Wang,
Chris Rook,

Examples

library(repfun)
library(dplyr)
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")