repfun (version 0.1.2)

ru_align: Align Columns for Reporting

Description

Pass in a data frame alignment criteria to have columns aligned for reporting.

Usage

ru_align(
  dsetin,
  varsin,
  byvars = NULL,
  alignment = "Right",
  compresschryn = "Y",
  ncspaces = 1
)

Value

A data frame based having the requested columns aligned for reporting.

Arguments

dsetin

The data set holding the columns to align.

varsin

Columns to align.

byvars

Set of group-by variables.

alignment

Type of alignment.

compresschryn

Compress by removing leading and trailing spaces for the resulting aligned column?

ncspaces

Number of spaces between N and Percent.

Author

Yongwei Wang,
Chris Rook,

Examples

#=================
# Adverse Events
#=================
library(repfun)
library(dplyr)
datdir <- file.path(gsub("\\","/",tempdir(),fixed=TRUE),"datdir")
dir.create(datdir,showWarnings=FALSE)
repfun::copydata(datdir)
rfenv <- repfun::rs_setup(D_POP="SAFFL",
                 D_POPLBL="Safety",
                 D_POPDATA=repfun::adsl %>% dplyr::filter(SAFFL =='Y'),
                 D_SUBJID=c("STUDYID","USUBJID"),
                 R_DICTION=NULL,
                 R_OTHERDATA=NULL,
                 R_INPUTDATA=NULL,
                 R_RAWDATA=NULL,
                 R_SDTMDATA=NULL,
                 R_ADAMDATA=datdir,
                 RetEnv=TRUE)
G_POPDATA <- rfenv$G_POPDATA %>% dplyr::mutate(TRT01AN=
                     ifelse(TRT01A=='Placebo',1,
                     ifelse(TRT01A=='Xanomeline Low Dose',2,3)))
attr(G_POPDATA$TRT01AN,"label") <- 'Actual Treatment for Period 01 (n)'
adae <- rfenv$adamdata$adae.rda() %>% dplyr::select(-SAFFL) %>%
        repfun::ru_getdata(G_POPDATA, c("STUDYID", "USUBJID"),
        keeppopvars=c("TRT01AN", "TRT01A"))
aesum_t <- repfun::ru_freq(adae,
              dsetindenom=G_POPDATA,
              countdistinctvars=c('STUDYID','USUBJID'),
              groupbyvarsnumer=c('TRT01AN','TRT01A','AEBODSYS','AEDECOD'),
              anyeventvars = c('AEBODSYS','AEDECOD'),
              anyeventvalues = c('ANY EVENT','ANY EVENT'),
              groupbyvarsdenom=c('TRT01AN'),
              resultstyle="NUMERPCT",
              totalforvar=c('TRT01AN'),
              totalid=99,
              totaldecode='Total',
              codedecodevarpairs=c("TRT01AN", "TRT01A"),
              varcodelistpairs=c(""),
              codelistnames=list(),
              resultpctdps=0) %>%
           repfun::ru_denorm(varstodenorm=c("tt_result", "PERCENT"),
                    groupbyvars=c("tt_summarylevel", "AEBODSYS", "AEDECOD"),
                    acrossvar="TRT01AN",
                    acrossvarlabel="TRT01A",
                    acrossvarprefix=c("tt_ac", "tt_p"))
print('Before Aligning')
print(head(aesum_t[,grep('(AEBODSYS|AEDECOD|tt_ac)',names(aesum_t))],20))
aesum_t_a <- repfun::ru_align(aesum_t, "tt_ac:")
print('After Aligning')
print(head(aesum_t_a[,grep('(AEBODSYS|AEDECOD|tt_ac)',names(aesum_t_a))],20))

#===========================
# Baseline Characteristics
#===========================
rfenv <- repfun::rs_setup(D_POP="SAFFL",
                 D_POPLBL="Safety",
                 D_POPDATA=repfun::adsl %>% dplyr::filter(SAFFL =='Y'),
                 D_SUBJID=c("STUDYID","USUBJID"),
                 R_DICTION=NULL,
                 R_OTHERDATA=NULL,
                 R_INPUTDATA=NULL,
                 R_RAWDATA=NULL,
                 R_SDTMDATA=NULL,
                 R_ADAMDATA=datdir,
                 RetEnv=TRUE)
G_POPDATA <- rfenv$G_POPDATA %>%
             dplyr::mutate(TRT01AN=ifelse(TRT01A=='Placebo',1,
                            ifelse(TRT01A=='Xanomeline Low Dose',2,3))) %>%
  repfun::ru_labels(varlabels=list('TRT01AN'='Actual Treatment for Period 01 (n)'))
demstats_t <- repfun::ru_sumstats(G_POPDATA,
                 analysisvars=c("AGE","TRTDURD"),
                 groupbyvars=c("STUDYID","TRT01AN"),
                 codedecodevarpairs=c("TRT01AN", "TRT01A"),
                 totalforvar="TRT01AN", totalid=99,
                 totaldecode="Total",
                 statsinrowsyn = "Y",
                 analysisvardps=list("AGE"=1,"TRTDURD"=2),
                 statslist=c("n", "mean", "median", "sd", "min", "max")) %>%
  repfun::ru_denorm(varstodenorm=c("tt_result"),
            groupbyvars=c("tt_avid", "tt_avnm", "tt_svid", "tt_svnm"),
            acrossvar="TRT01AN", acrossvarlabel="TRT01A",
            acrossvarprefix=c("tt_ac"))

print('Before Aligning')
print(head(demstats_t,10))
demstats_t_a <- repfun::ru_align(demstats_t, "tt_ac:", ncspaces=10)
print('After Aligning')
print(head(demstats_t_a,10))